item: #1 of 69 id: cord-000822-iuglkdcp author: Sperschneider, Jana title: Predicting pseudoknotted structures across two RNA sequences date: 2012-12-01 words: 5496 flesch: 55 summary: Single sequence structure prediction is always limited by the accuracy of the underlying folding model. The prediction results for single sequence structure prediction for each of the reference sequences with experimentally determined structures are also shown in Table 1 . keywords: alignment; dotknot; elements; prediction; pseudoknot; rna; sequence; structure cache: cord-000822-iuglkdcp.txt plain text: cord-000822-iuglkdcp.txt item: #2 of 69 id: cord-001835-0s7ok4uw author: None title: Abstracts of the 29th Annual Symposium of The Protein Society date: 2015-10-01 words: 138771 flesch: 38 summary: In conclusion, the analysis of hydropathic environments strongly suggests that the orientation of a residue in a three-dimensional structure is a direct consequence of its hydropathic environment, which leads us to propose a new paradigm, interaction homology, as a key factor in protein structure. In computer simulation modeling of protein structure in a solvent medium, explicit, implicit, effectivemedium, approaches are often adopted to incorporate the effects of solvation. keywords: acid; activation; activity; addition; affinity; amino; amyloid; analysis; antibodies; antibody; antigen; approach; assay; assembly; associated; bacterial; binding; biology; bonds; cancer; catalytic; cell; cellular; chain; changes; characterization; chemical; chemistry; coli; complex; computational; concentration; conditions; conformation; conserved; control; core; cross; crystal; crystal structure; data; department; determine; development; dimer; disease; disordered; disordered proteins; dna; docking; domain; drug; effect; energy; enzyme; essential; experiments; expression; factors; family; fluorescence; fluorescent protein; formation; forms; fragments; free; functions; gene; group; helix; human; hydrogen; hydrophobic; important; increase; inhibitors; institute; key; kinetic; level; ligand; light; like; lipid; loop; low; major; mass; mechanism; membrane protein; method; model; modification; molecular; molecules; motif; mutant; mutations; n protein; native; nature; new; nmr; non; novel; number; oligomers; order; pathways; peptide; potential; prediction; presence; present; process; processes; properties; protease; protein; protein aggregation; protein association; protein complexes; protein concentration; protein data; protein degradation; protein design; protein domain; protein dynamics; protein engineering; protein evolution; protein expression; protein families; protein folding; protein function; protein interactions; protein interface; protein kinases; protein molecules; protein production; protein sequences; protein stability; protein structure; protein surface; protein tyrosine; provide; range; ray; reaction; receptor; recognition; recombinant; region; regulation; research; residues; response; results; rna; role; self; sequence; set; shows; signal; signaling; simulations; site; size; solution; species; specific; specificity; spectroscopy; stability; state; step; structural; studies; study; substrate; subunit; surface; synthetic; system; target; target protein; tau protein; techniques; temperature; terminal; time; transcription; transfer; transition; transmembrane; type protein; understanding; unfolding; university; use; variants; virus; vitro; wild; work; yeast cache: cord-001835-0s7ok4uw.txt plain text: cord-001835-0s7ok4uw.txt item: #3 of 69 id: cord-002015-s3tdllby author: Burton, Aaron S. title: The elusive quest for RNA knots date: 2016-02-01 words: 3539 flesch: 47 summary: It also appears plausible that RNA knots, and other forms of entanglement, are not favored thermodynamically. Although RNA knots may be elusive today, it is conceivable that they were important in earlier evolutionary stages, even during the origins of life. keywords: dna; knots; knotted; proteins; rna; rnas; sequences; structures cache: cord-002015-s3tdllby.txt plain text: cord-002015-s3tdllby.txt item: #4 of 69 id: cord-002490-kw8psrmz author: Beniac, Daniel R. title: Structure of the Ebola virus glycoprotein spike within the virion envelope at 11 Å resolution date: 2017-04-11 words: 4085 flesch: 43 summary: Fields virology Ebola virus disease in West Africa-the first 9 months of the epidemic and forward projections Structural rearrangement of ebola virus VP40 begets multiple functions in the virus life cycle The organisation of Ebola virus reveals a capacity for extensive, modular polyploidy How do filovirus filaments bend without breaking ? Cellular entry of ebola virus involves uptake by a macropinocytosis-like mechanism and subsequent trafficking through early and late endosomes A system for functional analysis of Ebola virus glycoprotein Ebola virus enters host cells by macropinocytosis and clathrin-mediated endocytosis Inhibition of Ebola virus glycoprotein-mediated cytotoxicity by targeting its transmembrane domain and cholesterol Ebola virus entry requires the cholesterol transporter Niemann-Pick C1 Small molecule inhibitors reveal Niemann-Pick C1 is essential for Ebola virus infection Ebolavirus is internalized into host cells via macropinocytosis in a viral glycoprotein-dependent manner Cross-reactive and potent neutralizing antibody responses in human survivors of natural Ebolavirus infection Toremifene interacts with and destabilizes the Ebola virus glycoprotein Structural basis for Marburg virus neutralization by a cross-reactive human antibody Structures of protective antibodies reveal sites of vulnerability on Ebola virus Biochemical and structural characterization of cathepsin L-processed Ebola virus glycoprotein: implications for viral entry and immunogenicity Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor Ebola virus entry requires the host-programmed recognition of an intracellular receptor Role of endosomal cathepsins in entry mediated by the Ebola virus glycoprotein Endosomal proteolysis of the Ebola virus glycoprotein is necessary for infection The Primed Ebolavirus Glycoprotein (19-Kilodalton GP1, 2): Sequence and Residues Critical for Host Cell Binding Role of EXT1 and Glycosaminoglycans in the Early Stage of Filovirus Entry Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-A resolution Structure and orientation study of Ebola fusion peptide inserted in lipid membrane models Crystal structure of the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain The creation of stable cell lines expressing Ebola virus glycoproteins and the matrix protein VP40 and generating Ebola virus-like particles utilizing an ecdysone inducible mammalian expression system Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography Mapping of Ebolavirus Neutralization by Monoclonal Antibodies in the ZMapp Cocktail Using Cryo-Electron Tomography and Studies of Cellular Entry GraFix: sample preparation for single-particle electron cryomicroscopy The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy GP mRNA of Ebola Virus Is Edited by the Ebola Virus Polymerase and by T7 and Vaccinia Virus Polymerases 1 The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules Structure of glycosylated NPC1 luminal domain C reveals insights into NPC2 and Ebola virus interactions Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection Replication-deficient ebolavirus as a vaccine candidate EMAN: semiautomated software for high-resolution single-particle reconstructions SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields Architecture of the SARS coronavirus prefusion spike UCSF Chimera-a visualization system for exploratory research and analysis We would like to thank the Canadian Government Genomics Research and Development Initiative for funding, Dr. Steven Jones (National Microbiology Laboratory, Canada) for providing us with EBOV and Shannon Hiebert for excellent technical assistance. Marburg and Ebola viruses. keywords: domain; ebola; envelope; fig; images; mucin; resolution; spike; structure; virus cache: cord-002490-kw8psrmz.txt plain text: cord-002490-kw8psrmz.txt item: #5 of 69 id: cord-003020-q69f57el author: Farhadi, Tayebeh title: Computer-aided design of amino acid-based therapeutics: a review date: 2018-05-14 words: 8674 flesch: 36 summary: Designing proteins and peptides Molecular engineering: an approach to the development of general capabilities for molecular manipulation X-ray versus NMR structures as templates for computational protein design High-resolution protein design with backbone freedom Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design Backbone flexibility in computational protein design De novo computational design of retro-aldol enzymes One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions Search and sampling in structural bioinformatics The dead-end elimination theorem and its use in protein side-chain positioning Application of a self-consistent mean field theory to predict protein sidechains conformation and estimate their conformational entropy Design of protein-interaction specificity gives selective bZIP-binding peptides Computational methods for protein design and protein sequence variability: biased Monte Carlo and replica exchange Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm Side-chain and backbone flexibility in protein core design Dead-end elimination with a polarizable force field repacks PCNA structures Improved prediction of protein side-chain conformations with SCWRL4 Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences Computational design and characterization of a monomeric helical dinuclear metalloprotein Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure Achieving stability and conformational specificity in designed proteins via binary patterning Photophysics of a fluorescent non-natural amino acid: p-cyanophenylalanine An expanded eukaryotic genetic code A solvated rotamer approach to modeling watermediated hydrogen bonds at protein-protein interfaces Rotamer libraries in the 21st century Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library Potential energy functions for protein design De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions Structure by design: from single proteins and their building blocks to nanostructures Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor Using α-helical coiled coils to design nanostructured metalloporphyrin arrays Kemp elimination catalysts by computational enzyme design De novo design of a βαβ motif High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design Design of a novel globular protein fold with atomic-level accuracy Novel peptide-specific quantitative structure activity relationship (QSAR) analysis applied to collagen IV peptides with antiangiogenic activity Development of an informatics platform for therapeutic protein and peptide analytics Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions Recent development of peptide drugs and advance on theory and methodology of peptide inhibitor design Predicting the affinity of epitope-peptides with class I MHC molecule HLA-A*0201: an application of amino acid-based peptide prediction A brief overview of antimicrobial peptides containing unnatural amino acids and ligand-based approaches for peptide ligands Machine learning assisted design of highly active peptides for drug discovery PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides In silico predictions of 3D structures of linear and cyclic peptides with natural and nonproteinogenic residues Long-timescale molecular dynamics simulations of protein structure and function How fastfolding proteins fold Bond distances in polypeptide backbones depend on the local conformation Identification of tetrapeptides from a mixture based positional scanning library that can restore nM full agonist function of the L106P, I69T, I102S, A219V, C271Y, and C271R human melanocortin-4 polymorphic receptors (hMC4Rs) Protein design seeks to identify the properties of amino acid sequences that fold to predetermined structures with desirable structural and functional characteristics. keywords: acid; amino; amino acid; approach; binding; design; development; docking; drug; energy; interactions; methods; novel; peptide; peptidomimetics; protein; sequence; structure; therapeutics cache: cord-003020-q69f57el.txt plain text: cord-003020-q69f57el.txt item: #6 of 69 id: cord-004534-jqm1hxps author: None title: Abstract date: 2009-06-09 words: 139178 flesch: 39 summary: This simple model illustrates how differential detergent selectivity for faces and strong constraints coming from purely environmental features could influence transmembrane helix packing, membrane protein structure and assembly. Imaging of mobile stable lipid rafts in the live cell plasma membrane M. Brameshuber 1 , J. Weghuber 1 , V. Ruprecht 1 , H. Stockinger 2 , G. J. Schuetz 1 1 Johannes Kepler University Linz, Austria, 2 Medical University of Vienna, Austria The organization of the cellular plasma membrane at a nanoscopic length scale is believed to affect the association of distinct sets of membrane proteins for the regulation of multiple signaling pathways. keywords: acid; actin; activation; activity; addition; affinity; afm; aggregates; aggregation; amyloid; analysis; applications; approach; assembly; atomic; atp; behavior; bilayer; binding; biological; biology; biophysics; brain; calcium; cancer; cell; cell membrane; cell surface; center; chain; changes; channel; characterization; charge; chemical; chemistry; cholesterol; combination; complex; complexes; concentration; conditions; confocal; conformational; constant; contrast; control; correlation; cross; current; data; decrease; delivery; density; department; design; detection; development; diffusion; disease; distribution; dna; domain; drug; dynamics; effect; electron; emission; energy; environment; enzyme; excitation; experiments; expression; fibrils; field; flow; fluorescence; fluorescence microscopy; fluorescent protein; force; force microscopy; formation; france; free; fret; function; gene; genova; germany; group; growth; helix; human; imaging; increase; influence; institute; intensity; interaction; intracellular; italy; key; kinetics; laser; length; level; lifetime; ligand; light; lipid; lipid membranes; liposomes; living; measurements; mechanism; membrane; membrane protein; membrane surface; method; microscopy; model; model membrane; molecular; molecules; muscle; mutant; nanoparticles; neuronal; neurons; new; non; novel; number; order; parameters; particles; peptide; phase; physical; physics; plasma membrane; pore; potential; presence; present; probe; process; processes; properties; protein; protein complexes; protein dynamics; protein interactions; protein structure; range; rate; ray; reaction; receptor; region; release; report; research; residues; resolution; response; results; rna; role; sample; scanning; scattering; sciences; second; self; sequence; signal; simulations; site; size; solvent; species; specific; spectroscopy; stability; state; step; structure; studies; study; surface; system; target; techniques; temperature; terminal; time; transfer; transition; transmembrane; transport; treatment; type; understanding; unfolding; university; use; vesicles; virus; vitro; vivo; water; work cache: cord-004534-jqm1hxps.txt plain text: cord-004534-jqm1hxps.txt item: #7 of 69 id: cord-004584-bcw90f5b author: None title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date: 2011-08-06 words: 106959 flesch: 38 summary: to that of cell proteins (amide II band at *1550 cm -1 ) Membrane proteins and peptides are acting in an environment rich in other proteins or peptides. keywords: acid; actin; activation; activity; affinity; aggregation; amino; amyloid; analysis; applications; approach; assembly; associated; atomic; bilayer; binding; biological; cancer; cell; cell membrane; cell surface; chain; changes; channel; charge; chemical; cholesterol; complex; complexes; composition; compounds; concentration; conditions; conformational; control; correlation; data; delivery; detection; development; diffusion; distribution; dna; domain; drug; dynamics; effect; electron; energy; environment; enzyme; experiments; expression; fast; field; fluorescence; force; formation; free; function; fusion; gene; group; human; hydrophobic; imaging; increase; influence; institute; interaction; key; kinetics; laser; level; ligand; light; lipid; lipid membranes; liposomes; living; magnetic; major; measurements; mechanism; membrane; membrane binding; membrane interaction; membrane protein; membrane structure; membrane surface; method; microscopy; model; model membrane; molecular; molecules; nanoparticles; native; network; new; nmr; non; novel; number; order; organization; parameters; peptide; phase; plasma membrane; potential; presence; processes; properties; protein; protein complex; protein dynamics; protein interactions; protein structure; proton; range; rate; ray; reaction; receptor; region; regulation; research; residues; resolution; response; results; role; scattering; self; signal; simulations; sites; size; species; specific; spectra; spectroscopy; stability; state; structure; studies; study; substrate; surface; system; techniques; temperature; terminal; time; transfer; transition; transport; type; understanding; university; use; vesicles; vitro; vivo; water; work cache: cord-004584-bcw90f5b.txt plain text: cord-004584-bcw90f5b.txt item: #8 of 69 id: cord-007373-livz5zuu author: Gayathri, P. title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket date: 2006-03-15 words: 6254 flesch: 58 summary: SeMV protease belongs to the trypsin-like family of serine proteases. In the present study, the crystal structure of SeMV protease domain was determined to a resolution of 2.4 Å by multiple isomorphous replacement coupled with anomalous scattering, with a view to identify the residues involved in substrate binding as well as protease -VPg interactions. keywords: binding; cleavage; domain; fig; protease; protein; residues; semv; semv protease; serine; site; structure; vpg cache: cord-007373-livz5zuu.txt plain text: cord-007373-livz5zuu.txt item: #9 of 69 id: cord-008588-4eu9v5d3 author: Chastain, Michael title: Structural Elements in RNA date: 2008-02-29 words: 13702 flesch: 52 summary: The division of RNA structure into building blocks consisting of secondary or tertiary interactions makes it easier to describe RNA structures. Finally, the division of RNA structure into building blocks consisting of secondary or tertiary interactions makes it easier to describe RNA structures. keywords: base; bulge; dna; form; helix; hydrogen; interactions; junction; loop; nucleotides; protein; regions; rna; rna structure; structure; tertiary cache: cord-008588-4eu9v5d3.txt plain text: cord-008588-4eu9v5d3.txt item: #10 of 69 id: cord-009660-23cdi61w author: Györkey, Ferenc title: Electron microscopic observations on structures resembling myxovirus in human sarcomas date: 2006-06-27 words: 1887 flesch: 34 summary: T h e structures described in this paper may represent unenvelopecl ribonucleoprotein strands of an ubiquitous virus which is widely spread in human populations and seldom reaches full maturity. Preliminary findings concerning such structures, however, have recently been reported by Stewart36 who observed the occurrence of filamentous structures and budding type Clike virus particles in tissue cultures of human liposarcoma and Hodgkin's disease. keywords: structures; tumors; type; virus cache: cord-009660-23cdi61w.txt plain text: cord-009660-23cdi61w.txt item: #11 of 69 id: cord-010260-8lnpujip author: Anthonsen, Henrik W. title: The blind watchmaker and rational protein engineering date: 1994-08-31 words: 17358 flesch: 42 summary: A practical approach The modelling of electrostatic interactions in the function of globular proteins Electrostatic interactions in globular proteins: Calculation of the pH dependence of the redox potential of cytochrome C55 I Extracting information on folding from the amino acid sequence: Consensus regions with preferred conformation in homologous proteins Prediction of protein secondary structure at better than 70% accuracy Secondary structure prediction of all-helical proteins in two states PHD -An automatic mail server for protein secondary structure prediction Progress in protein structure prediction? Predicting protein secondary structure with a nearest-neighbor algorithm Database of homologyderived protein structures and the structural meaning of sequence alignment An winexpensive, versatile sample illuminator for photo-CIDNP on any NMR spectrometer Pancreatic lipases: Evolutionary intermediates in a positional change of catalytic carboxylates? key: cord-010260-8lnpujip authors: Anthonsen, Henrik W.; Baptista, António; Drabløs, Finn; Martel, Paulo; Petersen, Steffen B. title: The blind watchmaker and rational protein engineering date: 1994-08-31 journal: J Biotechnol DOI: 10.1016/0168-1656(94)90152-x sha: doc_id: 10260 cord_uid: 8lnpujip In the present review some scientific areas of key importance for protein engineering are discussed, such as problems involved in deducting protein sequence from DNA sequence (due to posttranscriptional editing, splicing and posttranslational modifications), modelling of protein structures by homology, NMR of large proteins (including probing the molecular surface with relaxation agents), simulation of protein structures by molecular dynamics and simulation of electrostatic effects in proteins (including pH-dependent effects). keywords: acid; alignment; amino; approach; cases; charge; data; engineering; et al; fig; gene; information; interactions; methods; modelling; nmr; number; potential; prediction; protein; protein engineering; protein sequence; protein structure; relaxation; residues; resonance; sequence; site; solution; solvent; structure; use cache: cord-010260-8lnpujip.txt plain text: cord-010260-8lnpujip.txt item: #12 of 69 id: cord-013387-q91052qw author: Leão, Rozires P. title: Identification of New Rofecoxib-Based Cyclooxygenase-2 Inhibitors: A Bioinformatics Approach date: 2020-08-26 words: 12146 flesch: 39 summary: The protonation state of ionizable residues of protein structure was analyzed using the PROPKA The bioactivity score of selected compounds was evaluated using the Molinspiration Server Cheminformatics tool (http://www.molinspiration.com) keywords: affinity; binding; compounds; drug; energy; hcox-2; inflammatory; inhibitors; interaction; ligand; lmqc36; lmqc50; lmqc72; protein; receptor; results; rofecoxib; score; structures; values cache: cord-013387-q91052qw.txt plain text: cord-013387-q91052qw.txt item: #13 of 69 id: cord-014685-ihh30q6f author: None title: Posters P788 - P999 date: 2005-09-21 words: 38408 flesch: 42 summary: 12 physical property parameters of protein structure were chosen to construct a 12-dimension physical property space. These systems have proven to be also valuable as membrane mimetic structures, as promising matrices for controlled-release and delivery of proteins, vitamins and small drugs in pharmacological applications, and they offer a 3D lipid matrix for successful crystallization of membrane proteins which do not easily crystallize in bulk solution. keywords: activity; aggregation; analysis; beta; binding; cells; changes; complex; complexes; concentration; conformational; data; delivery; dna; domain; drug; dynamics; effect; energy; experiments; folding; function; human; institute; interaction; light; lipid; loop; mechanism; membrane; membrane protein; method; model; molecular; native; new; nmr; order; peptide; phase; potential; presence; process; properties; protein; protein structure; region; residues; results; rna; rst; sequence; signi; site; solution; speci; stability; state; step; structure; studies; study; surface; system; temperature; terminal; time; transition; transport; type; unfolding; university; uorescence; water; work cache: cord-014685-ihh30q6f.txt plain text: cord-014685-ihh30q6f.txt item: #14 of 69 id: cord-015619-msicix98 author: None title: Virus Structure & Assembly date: 2009-02-24 words: 3306 flesch: 41 summary: Meshes and nanoindentation simulations are presented for several viruses: Hepatitis B, CCMV, HK97, and Phi 29. We demonstrate these methods using coarse-grained models of the assembly of icosahedral virus capsids as well as several simpler models of generic assembly chemistry. keywords: assembly; capsid; connector; dna; membrane; sars; structure; virus; viruses cache: cord-015619-msicix98.txt plain text: cord-015619-msicix98.txt item: #15 of 69 id: cord-015642-p46abodr author: Backofen, Rolf title: Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures date: 2013 words: 4204 flesch: 60 summary: Alg 2d meets 4g: G-quadruplexes in rna secondary structure prediction Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure The equilibrium partition function and base pair binding probabilities for RNA secondary structure RNA structure and the mechanisms of alternative splicing The secondary structure of RNA under tension Topology and prediction of RNA pseudoknots A practical guide to single-molecule FRET From sequences to shapes and back: a case study in RNA secondary structures Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches The ends of a large RNA molecule are necessarily close This work was supported in part by the Deutsche Forschungsgemeinschaft proj. Spatial distance can be approximated by the graph-distance in RNA secondary structure. keywords: base; distance; graph; rna; structure cache: cord-015642-p46abodr.txt plain text: cord-015642-p46abodr.txt item: #16 of 69 id: cord-017181-ywz6w2po author: Maus, Carsten title: Component-Based Modelling of RNA Structure Folding date: 2008 words: 5368 flesch: 48 summary: RNA structures are hierarchically organised (see figure 2 ). To allow RNA structures to escape from local energy minima and refold to more stable structures, the base pair dissociation time will be randomised, which leads to very short bonding times in some cases although the activation energy needed for opening the base pair is quite large. keywords: base; folding; level; macro; model; pair; ribosome; rna; simulation; structure; time cache: cord-017181-ywz6w2po.txt plain text: cord-017181-ywz6w2po.txt item: #17 of 69 id: cord-018133-2otxft31 author: Altman, Russ B. title: Bioinformatics date: 2006 words: 9594 flesch: 44 summary: Computer systems within bioinformatics thus must be able to handle biological sequence information effectively and efficiently. Nonetheless, the effects of sequence information on clinical databases will be significant. keywords: analysis; bioinformatics; data; databases; dna; function; genes; genome; human; information; knowledge; molecules; protein; sequence; structure cache: cord-018133-2otxft31.txt plain text: cord-018133-2otxft31.txt item: #18 of 69 id: cord-018401-josb16pi author: Kumaraswamy, Priyadharshini title: Hierarchical Self-Assembled Peptide Nano-ensembles date: 2014-03-01 words: 13493 flesch: 41 summary: A bioactive self-assembled membrane to promote angiogenesis Morphology of self-assembled structures formed by short peptides from the amyloidogenic protein tau depends on the solvent in which the peptides are dissolved Time-lapse atomic force microscopy in the characterization of amyloid-like fibril assembly and oligomeric intermediates Using the bending beam model to estimate the elasticity of diphenylalanine nanotubes Nanostructured films from hierarchical self-assembly of amyloidogenic proteins Transthyretin fibrillogenesis entails the assembly of monomers: a molecular model for in vitro assembled transthyretin amyloid-like fibrils Self-assembled peptide nanotubes as an etching material for the rapid fabrication of silicon wires Confined conversion of CuS nanowires to CuO nanotubes by annealinginduced diffusion in nanochannels Electrochemical determination of dopamine based on selfassembled peptide nanostructure Natural tri-to hexapeptides self-assemble in water to amyloid beta-type fiber aggregates by unexpected alpha-helical intermediate structures William Thomas Astbury 1898-1961 Hierarchical self-assembly of Tjernberg peptide at nanoscale Conformational transition of amyloid beta-peptide Connecting macroscopic observables and microscopic assembly events in amyloid formation using coarse grained simulations Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences Stability of diphenylalanine peptide nanotubes in solution Molecular dynamics simulation of the α-helix to β-sheet transition in coiled protein filaments: evidence for a critical filament length scale Rigid self-assembled hydrogel composed of a modified aromatic dipeptide From the globular to the fibrous state: protein structure and structural conversion in amyloid formation Amyloid fibrillogenesis: themes and variations Protein misfolding and disease; protein refolding and therapy The correctly-folded state of proteins: Is it a metastable state? Direct conversion of an oligopeptide from a ß-sheet to an a-helix: a model for amyloid formation Identification of a penta-and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties Conformational transitions and fibrillation mechanism of human calcitonin as studied by high-resolution solid-state 13C NMR Charge attraction and beta propensity are necessary for amyloid fibril formation from tetrapeptides Self-assembly of a modified amyloid peptide fragment: pH responsiveness and nematic phase formation Controlling amyloid growth in multiple dimensions Templating molecular arrays in amyloid's crossbeta grooves Effect of PEG crystallization on the self-assembly of PEG/peptide copolymers containing amyloid peptide fragments Molecular self-assembly of peptide nanostructures: mechanism of association and potential uses Puramatrix: Self-assembling peptide nanofiber scaffolds Rational design and application of responsive alpha-helical peptide hydrogels Lipid-like self-assembling peptides Production of self-assembling biomaterials for tissue engineering Light harvesting antenna on an amyloid scaffold Dual-surface modification of the tobacco mosaic virus Neural stem cells encapsulated in a functionalized self-assembling peptide hydrogel for brain tissue engineering Fine-tuning the pH trigger of self-assembly Artificial transmembrane ion channels from self-assembling peptide nanotubes Self-assembling chimeric polypeptidedoxorubicin conjugate nanoparticles that abolish tumours after a single injection A novel vaccine using nanoparticle platform to present immunogenic M2e against avian influenza infection Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine Development of an electrochemical metal-ion biosensor using self-assembled peptide nanofibrils Self-assembled diphenylalanine nanowires for cellular studies and sensor applications An auto-biotinylated bifunctional protein nanowire for ultra-sensitive molecular biosensing Remote electronic control of DNA hybridization through inductive coupling to an attached metal nanocrystal antenna Design of metal-binding sites onto self-assembled peptide fibrils Self-assembling peptide-based nanostructures for regenerative medicine Self-assembly of collagen-mimetic peptide amphiphiles into biofunctional nanofiber Self-assembling functionalized nanopeptides for immediate hemostasis and accelerative liver tissue regeneration However, there are certain limitations associated with this technique, too, such as a limited resolution, strong dependency of the quality of predictions on the size of the peptide, and the limited number of peptide residues for which such predictions could be made. keywords: acid; amino; amyloid; assembly; beta; cell; fibrils; form; formation; hydrogen; hydrophobic; interactions; microscopy; nanostructures; nanotubes; peptide; peptide self; peptide structures; protein; residues; self; sequence; sheet; structures; surface cache: cord-018401-josb16pi.txt plain text: cord-018401-josb16pi.txt item: #19 of 69 id: cord-018963-2lia97db author: Xu, Ying title: Protein Structure Prediction by Protein Threading date: 2010-04-29 words: 15314 flesch: 39 summary: The protein threading problem with sequence amino acid interaction preferences is NP-complete Introduction to ProteinArchitecture: The StructuralBiology ofProteins A unified statistical framework for sequence comparison and structure comparison Emergence of preferred structures in a simple model of protein folding Are protein folds atypical? Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix A distance-dependent atomic knowledge-based potential for improved protein structure selection Geometric cooperativity and anti-cooperativity of threebody interactions in native proteins Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome Protein distance constraints predicted by neural networks and probability density functions Peons: A neuralnetwork-based consensus predictor that improves fold recognition Threading analysis suggests that the obese gene product may be a helical cytokine Comparative genomics ofthe Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell How many species are there on earth Improvement ofthe GenTHREADER method for genomic fold recognition Protein Structure Prediction by Protein Threading The Genomic Threading Database: A comprehensive resource for structural annotations of the genomes from key organisms Novel knowledge-based mean force potential at atomic level Statistical significance of protein structure prediction by threading Statistical significance of hierarchical multibody potentials based on Delaunay tessellation and their application in sequence-structure alignment SCOP: A structural classification of proteins database for the investigation of sequences and structures Protein superfamilies and domain superfolds CATH-A hierarchic classification of protein domain structures A local alignment method for protein structure motifs Threading with explicit models for evolutionary conservation ofstructure and sequence Combination ofthreading potentials and sequence profiles improves fold recognition Combinatorial Optimization: Algorithms and Complexity New techniques in structural NMR-anisotropic interactions Protein fold recognition through application of residual dipolar coupling data Protein structure prediction using sparse dipolar coupling data The anatomy and taxonomy ofprotein structure Graph minors .2. To keep up with the rate at which protein structures are being solved, there is a clear need for more automated domain-partitioning methods to process the newly solved structures. keywords: algorithm; alignment; amino; decomposition; energy; et al; families; fold; function; graph; number; prediction; problem; protein; protein structure; protein threading; query; sequence; structure; template; threading; tree cache: cord-018963-2lia97db.txt plain text: cord-018963-2lia97db.txt item: #20 of 69 id: cord-022494-d66rz6dc author: Webb, B. title: Comparative Modeling of Drug Target Proteins date: 2014-10-01 words: 8784 flesch: 45 summary: 19, 20 Computational protein structure prediction methods, such as threading 21 and comparative protein structure modeling, 22, 23 strive to bridge the sequence-structure gap by utilizing these evolutionary relationships. 9 Shown are the different ranges of applicability of comparative protein structure modeling, threading, and de novo structure prediction, their corresponding accuracies, and their sample applications. keywords: accuracy; alignment; docking; drug; errors; identity; ligand; methods; modeling; models; protein; sequence; structure; target; template cache: cord-022494-d66rz6dc.txt plain text: cord-022494-d66rz6dc.txt item: #21 of 69 id: cord-023208-w99gc5nx author: None title: Poster Presentation Abstracts date: 2006-09-01 words: 71178 flesch: 41 summary: Peptide structures can be approached by spectroscopy and NMR techniques but data from these approaches too frequently diverge. To increase the stability and the therapeutic efficacy of peptide sequences from myelin oligodendrocyte protein (MOG) that act as multiple sclerosis (MS) antigens, we grafted them onto a framework of a particularly stable class of peptides, the cyclotides. keywords: acid; activation; activity; affinity; aggregation; aim; alpha; amino; amino acid; analogues; analysis; approach; arg; assay; beta; binding; blood; bond; cancer; cell; chain; chemical; chemistry; complex; complexes; compounds; concentration; conformational; conjugates; cyclic; data; derivatives; design; development; disulfide; dna; domain; effect; enzyme; epitope; fmoc; fragment; gly; group; growth; hplc; human; inhibitors; integrin; interaction; ligands; mechanism; membrane; method; mice; model; molecular; molecules; native; new; nmr; non; novel; opioid; order; patients; peptide; peptide analogues; peptide chain; peptide synthesis; phase; phase peptide; phe; position; potential; prepared; presence; products; proline; properties; protein; reaction; receptor; residues; results; role; sequence; site; solution; specific; spectroscopy; stability; strategy; structure; studies; study; surface; synthetic; system; target; terminal; therapeutic; treatment; tumor; turn; type; tyr; use; vivo; water; work cache: cord-023208-w99gc5nx.txt plain text: cord-023208-w99gc5nx.txt item: #22 of 69 id: cord-023209-un2ysc2v author: None title: Poster Presentations date: 2008-10-07 words: 112272 flesch: 42 summary: A specifi c bioassay was developed for screening peptides activity in high salinity conditions in order to evaluate the inhibition of biofi lm growth, based on growing biofi lmforming bacteria in a 96-wells microtiter plate. The insight into the molecular mechanism of peptides activity is obtained in vitro using SAXS method and artifi cial systems mimicking a bacterial cytoplasmic membrane. keywords: acid peptide; acid residues; acids; activation; activities; activity; affi; agents; aggregation; aim; ala; amide; amino; amino acid; amyloid; analogs; analogues; analysis; antimicrobial; application; approach; assay; backbone; binding; biological; blood; bond; brain; c peptide; cancer; cation; cell; chemical; chemistry; cient; city; coil; complex; compounds; concentration; conditions; confi; conformational; conjugates; coupling; cyclic; data; delivery; derivatives; design; development; diseases; dna; domain; drug; ed peptides; effect; effi; experiments; family; fmoc; formation; fragments; free; function; gly; group; helix; hplc; human; identifi; infl; inhibition; inhibitors; interaction; interest; leu; ligation; lipid; mass; mechanism; membrane; method; microwave; model; model peptides; modifi; modifi ed; molecules; native; natural; new; nity; nmr; non; novel; number; order; peptide; peptide analogues; peptide bond; peptide chain; peptide chemistry; peptide fragments; peptide library; peptide ligands; peptide sequence; peptide structure; peptide synthesis; phase peptide; phase synthesis; phe; position; positive; potential; presence; present; process; processes; properties; protein; purifi; range; reaction; receptor; recognition; region; report; residues; results; role; rst; selective; sequence; signifi; site; solution; specifi c; spectroscopy; stability; stable; strategy; structure; studies; study; surface; synthetic; system; target; terminal; terminus; therapy; time; treatment; trp; tumor; type; university; uorescence; uptake; use; vitro; vivo; water; work cache: cord-023209-un2ysc2v.txt plain text: cord-023209-un2ysc2v.txt item: #23 of 69 id: cord-023225-5quigar4 author: None title: Posters date: 2012-08-21 words: 70555 flesch: 41 summary: Aim of this study is the introduction, in the type 1' β turn peptide structure, of the sugar moiety specific for anti-gangliosides antibody recognition by synthesizing specific building blocks. Peptide synthesis was used to verify the accuracy of the determined sequence and to prepare sufficient peptide amount for biological activity studies. keywords: acid; activity; addition; affinity; agents; aggregation; aib; aim; amino; amino acid; amyloid; analogs; analogues; analysis; approach; bacteria; binding; biological; blood; bond; cancer; cell; chain; chemical; chemistry; class; complex; compounds; conditions; conformation; cyclic; cys; data; derivatives; design; development; disease; disulfide; dna; drug; effect; fmoc; formation; function; gly; group; helical; helix; human; hydrophobic; increase; inhibitor; interactions; leu; linear; mechanism; membrane; method; model; moiety; molecules; new; nmr; non; novel; order; peptide; peptide analogues; peptide sequence; peptide synthesis; phase; phase peptide; phe; position; potential; presence; present; process; properties; protein; reaction; receptor; residues; resin; results; role; selective; selectivity; sequence; series; site; solution; specific; specificity; stability; strategy; structure; studies; study; synthetic; system; target; terminal; terminus; treatment; type; university; use; vivo; water; work cache: cord-023225-5quigar4.txt plain text: cord-023225-5quigar4.txt item: #24 of 69 id: cord-023284-i0ecxgus author: None title: Abstracts of publications related to QASR date: 2006-09-19 words: 19972 flesch: 40 summary: The systems allow interactive data communication among the simulation programs for their strategically combined use; e) The structure and functions of MolWorld is illustrated on modeling the alanine molecule: (i) data model of molecular structures; (ii) chemical formula input; (iii) generation of 3D molecular structure; (iv) formulation of bonding model; (v) interactive molecular orbital graphics; (vi) methods of visualizing electronic structures; (vii) use of molecular orbital graphics for chemical reactions. Title: Retention prediction of analytes in reversed-phase high-performance liquid chromatography based on molecular structure. keywords: activity; analysis; atoms; binding; chemical; compounds; conformations; crystal; data; descriptors; distance; energy; fig; group; linear; logp; method; model; modeling; molecular; molecules; nmr; number; parameters; protein; ray; receptor; relat; results; ring; set; site; solution; steric; structure; substituent; title; type; values cache: cord-023284-i0ecxgus.txt plain text: cord-023284-i0ecxgus.txt item: #25 of 69 id: cord-023442-4vzwc2d2 author: None title: Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA date: 2006-12-05 words: 55600 flesch: 45 summary: Applications include both thin-film and bulk x-ray microanalysis and examples of contrast in backscattered electron images obtained in the SEM. The effects of adjusting the Wehnelt-to-tip distance vary for different electron microscope systems. keywords: addition; analysis; associated; atomic; backscattered; carlo; cells; chemical; comparison; composition; conditions; confocal; contrast; cross; crystal; data; detection; detector; developed; development; distribution; drying; effects; electron; electron beam; electron microscopy; energy; field; fig; figure; form; formation; glass; image; imaging; laser; light; lines; material; measurement; method; microscope; milk; model; monte; new; number; particles; pattern; phase; point; preparation; probe; process; program; ray; region; resolution; results; sample; scanning; scattering; sections; sem; signal; silicon; simulation; size; specific; specimen; structures; studies; study; substrate; supplement; surface; system; techniques; temperature; time; tissue; transmission electron; type; use; vol; water; work cache: cord-023442-4vzwc2d2.txt plain text: cord-023442-4vzwc2d2.txt item: #26 of 69 id: cord-023726-2fduzqyb author: STRAUSS, JAMES H. title: The Structure of Viruses date: 2012-07-27 words: 10619 flesch: 54 summary: The two families of enveloped DNA viruses that we consider here, the poxviruses and the herpesviruses, contain large genomes and complicated virus structures. The structure of most enveloped viruses is not as rigorously constrained as that of icosahedral virus particles. keywords: assembly; budding; cell; enveloped; fig; form; glycoproteins; membrane; nucleocapsid; protein; rna; structure; symmetry; virion; viruses cache: cord-023726-2fduzqyb.txt plain text: cord-023726-2fduzqyb.txt item: #27 of 69 id: cord-031957-df4luh5v author: dos Santos-Silva, Carlos André title: Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era date: 2020-09-02 words: 16639 flesch: 34 summary: Thus, there is a need for computational framework methods to predict protein structures based on the knowledge of the sequence. In addition, in recent years, there has been impressive progress in the development of algorithms for protein folding that may aid in the prediction of protein structures from amino acid sequence information. keywords: acid; activity; amps; analysis; antifungal; approaches; binding; bonds; cysteine; database; defensins; disulfide; docking; family; figure; function; gene; identification; information; lipid; methods; modeling; models; motif; novel; pathogen; peptides; plant; potential; prediction; present; protein; residues; sequence; structure cache: cord-031957-df4luh5v.txt plain text: cord-031957-df4luh5v.txt item: #28 of 69 id: cord-033010-o5kiadfm author: Durojaye, Olanrewaju Ayodeji title: Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study date: 2020-10-02 words: 8149 flesch: 48 summary: Qualitative Model Energy Analysis (QMEAN) is a composite scoring function that describes protein structures on the basis of major geometrical aspects. A novel coronavirus and SARS Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide Dissection study on the SARS 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly-specific protease inhibitors 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism Only one protomer is active in the dimer of SARS 3C-like proteinase Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase A trial of lopinavir-ritonavir in adults hospitalized with severe covid-19 EMBOSS: the European molecular biology open software suite SRS, an indexing and retrieval tool for flat file data libraries Issues in bioinformatics benchmarking: the case study of multiple sequence alignment HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Toward the estimation of the absolute quality of individual protein structure models MolProbity: more and better reference data for improved all-atom structure validation Chapter 2: Protein Composition and Structure Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology UCSF chimera-a visualization system for exploratory research and analysis Fasman GD (1974) Prediction of protein conformation Protein Identification and Analysis Tools on the ExPASy Server The rapid generation of mutation data matrices from protein sequences MEGA7: keywords: 2019; acid; amino; amino acid; binding; coronavirus; docking; model; ncov; protein; proteinase; sars; score; sequence; structure; target protein; template cache: cord-033010-o5kiadfm.txt plain text: cord-033010-o5kiadfm.txt item: #29 of 69 id: cord-102463-d440jsek author: Eguchi, Raphael R. title: IG-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation date: 2020-08-10 words: 5165 flesch: 39 summary: eLife Critical assessment of methods of protein structure prediction (CASP)-Round XIII RosettaBackrub-a web server for flexible backbone protein structure modeling and design Evaluation of protein engineering and process optimization approaches to enhance antibody drug manufacturability Predictive tools for stabilization of therapeutic proteins Post-translational Modifications of Recombinant Proteins: Significance for Biopharmaceuticals General strategy for the generation of human antibody variable domains with increased aggregation resistance We thank Sergey Ovchinnikov for helpful discourse during early phases of this project, and for contributing initial code that became part of the torsion-reconstruction loss function. To address this fundamental challenge in modeling protein structure, we explore the use of deep neural networks to infer a continuous structural space in which we can smoothly interpolate between different backbone conformations. keywords: backbone; design; distance; figure; generative; model; protein; space; structures; training; vae cache: cord-102463-d440jsek.txt plain text: cord-102463-d440jsek.txt item: #30 of 69 id: cord-103823-3rchp9yy author: Taufer, Michela title: RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology date: 2008-11-30 words: 10174 flesch: 47 summary: Mechanisms and enzymes involved in SARS coronavirus genome expression Stem-loop structures in prokaryotic genomes An atypical RNA pseudoknot simulator and an upstream attenuation signal for À1 ribosomal frameshifting of SARS coronavirus A pseudoknot in the 3 0 non-core region of the glmS ribozyme enhances self-cleavage activity Simultaneous solution of the RNA folding, alignment, and protosequence problems Computer prediction of RNA structure Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide A dynamic programming algorithm for RNA structure prediction including pseudoknots Design, implementation, and evaluation of a practical pseudoknot folding algorithm based on thermodynamics ILM: a web server for predicting RNA secondary structures with pseudoknots HotKnots: heuristic prediction of RNA secondary structures including pseudoknots PseudoBase: a database with RNA pseudoknots Palindromes in SARS and other coronaviruses CompPknots: a framework for parallel prediction and comparison of RNA secondary structures with pseudoknots An algorithm for comparing multiple RNA secondary structures Comparing multiple RNA secondary structures using tree comparisons Predictor@Home: a protein structure prediction supercomputer based on global computing Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide distributed computing Vienna RNA secondary structure server RNA secondary structure prediction using stochastic context-free grammars and evolutionary history CONTRAfold: RNA secondary structure prediction without physics-based models Exploring the space of RNA secondary structure motifs using suffix arrays Identification of consensus RNA secondary structures using suffix arrays Comparison of the predicted and observed secondary structure of T4 phage lysozyme Depth annotation of RNA folds for secondary structure motif search RNA motif search using the structure to string str 2 method Nonrandom clusters of palindromes in herpesvirus genomes NuPack: a software suite for the analysis and design of nucleic acids Distributed computing in practice: the Condor experience BOINC: a system for public-resource computing and storage PseudoViewer2: visualization of RNA pseudoknots of any type Identification of common molecular subsequences A general method applicable to the search for similarities in the amino acid sequences of two proteins An approach to selecting putative RNA motifs using MDL principle Nodamura virus from Japan: a new and unusual arbovirus resistant to diethyl ether and chloroform A small RNA virus with a divided genome from Heteronychus arator (F.) Previously, grid technology was applied successfully to protein structure prediction [17, 18] and similar achievements are expected for RNA secondary structure prediction. keywords: algorithm; computing; fig; motifs; nucleotides; pknots; prediction; pseudoknots; replication; rna; rnavlab; segments; sequences; structures; virus cache: cord-103823-3rchp9yy.txt plain text: cord-103823-3rchp9yy.txt item: #31 of 69 id: cord-171099-d0qr84xg author: Buehler, Markus J. title: Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date: 2020-03-30 words: 4514 flesch: 41 summary: Natur, acatec Ultrathin Free-Standing Bombyx mori Silk Nanofibril Membranes Deformation and failure of protein materials in physiologically extreme conditions and disease Silk-Its Mysteries, How It Is Made, and How It Is Used Materials by design: Merging proteins and music Materiomics: An -omics approach to biomaterials research Nature's hierarchical materials Predictive modelling-based design and experiments for synthesis and spinning of bioinspired silk fibres A series of PDB related databases for everyday needs Structure and stability of the lamin A tail domain and HGPS mutant Evaluating Hierarchical Structure in Music Annotations Sounds interesting: can sonification help us design new proteins? Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence Sonification based de novo protein design using artificial intelligence, structure prediction and analysis using molecular modeling E-MSD: an integrated data resource for bioinformatics Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features The anisotropic network model web server at 2015 (ANM 2.0) Presenting musical encoding in two versions - one in the amino-acid scale and one based on equal temperament tuning - the method allows for expressing protein structures in audible space, offering novel avenues to represent, analyze and design architectural features across length- and time-scales. keywords: amino; figure; music; protein; sound; spike; structure; vibrational; virus cache: cord-171099-d0qr84xg.txt plain text: cord-171099-d0qr84xg.txt item: #32 of 69 id: cord-251982-vbchjexm author: Sarikavak-Lisesivdin, B. title: Structural parameters and electronic properties of 2D carbon allotrope: graphene with a kagome lattice structure date: 2020-09-17 words: 2197 flesch: 48 summary: Bond lengths, electronic band structure, and projected density of states were calculated. Electronic band structure calculations show kagome flat-band formation with higher d-orbital contributed bonding behavior than the pristine graphene structure. keywords: band; carbon; graphene; kagome; structure cache: cord-251982-vbchjexm.txt plain text: cord-251982-vbchjexm.txt item: #33 of 69 id: cord-252166-qah877pk author: Ekins, S title: In silico pharmacology for drug discovery: applications to targets and beyond date: 2007-09-01 words: 12716 flesch: 32 summary: However, such pharmacological targets have been difficult for in silico methods to derive small molecule inhibitors owing to generally quite shallow binding sites. For example, the work of Fliri et al. (2005b) presented the biological spectra for a cross-section of the proteome. keywords: activity; binding; compounds; database; design; discovery; drug; et al; human; inhibitors; methods; models; molecular; molecules; novel; pharmacology; pharmacophore; protein; qsar; receptor; screening; set; silico; structure; targets cache: cord-252166-qah877pk.txt plain text: cord-252166-qah877pk.txt item: #34 of 69 id: cord-254107-02bik024 author: Hillisch, Alexander title: Utility of homology models in the drug discovery process date: 2004-08-31 words: 7383 flesch: 38 summary: An Introduction The response of protein structures to amino-acid sequence changes Fold Recognition Methods Progress in protein structure prediction Assessment of homology-based predictions in CASP5 SCOP: a structural classification of proteins database for the investigation of sequences and structures Databases for protein-ligand complexes LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures PDBsum: summaries and analyses of PDB structures MODBASE, a database of annotated comparative protein structure models, and associated resources Comparative protein modelling by satisfaction of spatial restraints The SWISS-MODEL Repository of annotated threedimensional protein structure homology models Supporting your pipeline with structural knowledge There are numerous examples where protein homology models have supported the discovery and the optimization of lead compounds with respect to potency and selectivity. keywords: binding; compounds; design; discovery; drug; homology; homology models; human; modeling; models; protein; receptor; sequence; structure; target cache: cord-254107-02bik024.txt plain text: cord-254107-02bik024.txt item: #35 of 69 id: cord-257494-242k58ll author: Bastos, Paulo title: Human Antimicrobial Peptides in Bodily Fluids: Current Knowledge and Therapeutic Perspectives in the Postantibiotic Era date: 2017-01-17 words: 17385 flesch: 26 summary: A new skin-specific proteinase inhibitor that is a target for crosslinking by transglutaminase Peptide hormones and their analogues: Distribution, clearance from the circulation, and inactivation in vivo Discovery of JANUVIA (Sitagliptin), a selective dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes Human antimicrobial peptides and proteins Antimicrobial peptides: Properties and applicability Structures of human host defense cathelicidin LL-37 and its smallest antimicrobial peptide KR-12 in lipid micelles Human antimicrobial peptides (AMPs) represent approximately 10% of all curated AMPs catalogued to date. keywords: abps; acids; action; activity; amino; amps; aureus; bacteria; cationic; cells; coli; defensins; fluids; gram; histatin; host; human; identification; infection; ll-37; membrane; novel; peptides; plasma; properties; protein; residues; resistance; salivary; species; structure cache: cord-257494-242k58ll.txt plain text: cord-257494-242k58ll.txt item: #36 of 69 id: cord-263017-rh86g4jk author: Wigginton, Krista Rule title: Virus disinfection mechanisms: the role of virus composition, structure, and function date: 2011-12-09 words: 3714 flesch: 22 summary: This knowledge will allow for physical/chemical descriptions of virus inactivation and thus further our understanding of virus disinfection to the most basic mechanistic level. This knowledge will allow for physical/chemical descriptions of virus inactivation and thus further our understanding of virus disinfection to the most basic mechanistic level. keywords: capsid; chlorine; disinfection; genome; inactivation; poliovirus; protein; structure; virus cache: cord-263017-rh86g4jk.txt plain text: cord-263017-rh86g4jk.txt item: #37 of 69 id: cord-264489-h1n9ywbd author: Roy, Urmi title: Insight into the Structures of Interleukin-18 Systems date: 2020-07-31 words: 4352 flesch: 43 summary: Holt The structure and binding mode of interleukin-18 Expression, purification and structural analysis of human IL-18 binding protein: a potent therapeutic molecule for allergy Structural basis for antagonism of human interleukin 18 by poxvirus interleukin 18-binding protein MEGA7: The ligand bound holo forms of IL-18/IL-18R are also elucidated by binding protein (IL-18BP) is a cell surface receptor that binds to and eventually leads to IL-18 neutralization (Dinarello et al. 2013) . keywords: binding; complex; dynamics; et al; il-18; interactions; ligand; protein; receptor; residues; roy; structure cache: cord-264489-h1n9ywbd.txt plain text: cord-264489-h1n9ywbd.txt item: #38 of 69 id: cord-266543-ng9zr299 author: Klebe, Gerhard title: Virtual ligand screening: strategies, perspectives and limitations date: 2006-06-20 words: 11104 flesch: 38 summary: Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor Docking ligands onto binding site representations derived from proteins built by homology modelling Ligand-supported homology modelling of protein binding sites using knowledge-based potentials Implications of protein flexibility for drug discovery Molecular docking to ensembles of protein structures Ligand docking to proteins with discrete side-chain flexibility FlexE: efficient molecular docking considering protein structure variations Testing a flexible-receptor docking algorithm in a model binding site Accommodating protein flexibility in computational drug design Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case Probing flexibility and 'induced-fit' phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations Unveiling the full potential of flexible receptor docking using multiple crystallographic structures Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes Expect the unexpected or caveat for drug designers: multiple structure determinations using aldose reductase crystals treated under varying conditions pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design Understanding protein-ligand interactions: the price of protein flexibility ZZ Made EZ: influence of inhibitor configuration on enzyme selectivity Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition Approaches to the description and prediction of binding affinity of small-molecule ligands to macromolecular receptors Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity Predicting binding modes, binding affinities and 'hot spots' for protein-ligand complexes using a knowledge-based scoring function A computational procedure for determining energetically favorable binding sites on biologically important macromolecules SuperStar: a knowledge based approach for identifying interaction sites in proteins Knowledge-based scoring function to predict proteinligand interactions Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions Utilising structural knowledge in drug design strategies: applications using Relibase ZINC-a free database of commercially available compounds for virtual screening The art and practice of structure-based drug design: a molecular modelling perspective Fragment-based drug discovery Fragment-based lead discovery Current trends in lead discovery: are we looking for the appropriate properties? Consideration of such criteria will drive docking solutions especially into regions either frequently trapped by other bound ligands or featured by complementary analytical tools as being particularly relevant for binding. keywords: analysis; binding; compounds; crystal; data; discovery; docking; drug; ligand; molecules; pocket; protein; scoring; screening; site; structure; target; water cache: cord-266543-ng9zr299.txt plain text: cord-266543-ng9zr299.txt item: #39 of 69 id: cord-266921-x9q7dwc4 author: Worrall, Jonathan AR title: Information available at cut rates: structure and mechanism of ribonucleases date: 2006-12-26 words: 4617 flesch: 41 summary: The apparent wanton destruction of RNA by ribonucleases poses several questions: how do cells maintain folded RNA structures, such as tRNA and ribosomes, in the presence of all these keen ribonucleases? The crystal structure of the RNase E catalytic domain has been solved in complex with RNA substrate at 2.85 Å (Figure 1a ) keywords: coli; crystal; exosome; figure; fold; mechanism; processing; ribonucleases; rnase; site; structure cache: cord-266921-x9q7dwc4.txt plain text: cord-266921-x9q7dwc4.txt item: #40 of 69 id: cord-270587-k56fze59 author: Scherbinina, Sofya I. title: Three-Dimensional Structures of Carbohydrates and Where to Find Them date: 2020-10-18 words: 12396 flesch: 26 summary: The majority of existing repositories for carbohydrate 3D structures offer open-access data via web interface. The majority of existing repositories for carbohydrate 3D structures offer open-access data via web interface. keywords: analysis; bank; carbohydrate; complexes; data; database; dynamics; energy; field; figure; force; glycan; glycoproteins; interactions; modeling; molecular; nmr; oligosaccharides; pdb; protein; simulations; software; structure; table; tools; visualization; web cache: cord-270587-k56fze59.txt plain text: cord-270587-k56fze59.txt item: #41 of 69 id: cord-278135-kvuti410 author: Benjin, Xu title: Developments, applications, and prospects of cryo‐electron microscopy date: 2019-12-26 words: 6416 flesch: 38 summary: 1 3D reconstruction is used to deduce 3D structure from 2D images. Also one needs to transform 2D images into 3D structure. keywords: complex; cryo; development; electron; em structure; human; molecular; protein; resolution; sample; structure cache: cord-278135-kvuti410.txt plain text: cord-278135-kvuti410.txt item: #42 of 69 id: cord-282035-jibmg4ch author: Dunbar, R. I. M. title: Structure and function in human and primate social networks: implications for diffusion, network stability and health date: 2020-08-26 words: 11521 flesch: 44 summary: Phil The brain structural disposition to social interaction Amygdala volume and social network size in humans Intrinsic amygdala-cortical functional connectivity predicts social network size in humans Ventromedial prefrontal volume predicts understanding of others and social network size 2012 Orbital prefrontal cortex volume predicts social network size: an imaging study of individual differences in humans Online social network size is reflected in human brain structure Neural connections foster social connections: a diffusion-weighted imaging study of social networks Social brain volume is associated with in-degree social network size among older adults The structural and functional brain networks that support human social networks Gray matter volume of the anterior insular cortex and social networking 2020 10,000 social brains: sex differentiation in human brain anatomy Social network size affects neural circuits in macaques In press. Organizational complexity and demographic scale in primary states Organizational structure and scalar stress Primate social group sizes exhibit a regular scaling pattern with natural attractors Network scaling reveals consistent fractal pattern in hierarchical mammalian societies Neocortex size and social network size in primates Stepwise evolution of stable sociality in primates Discrete hierarchical organization of social group sizes 2020 keywords: brain; community; effect; family; friends; group; human; individuals; information; layer; networks; number; primates; relationships; size; structure; ties; time; trust cache: cord-282035-jibmg4ch.txt plain text: cord-282035-jibmg4ch.txt item: #43 of 69 id: cord-283491-y6t64pux author: Brzezinski, Dariusz title: Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models date: 2020-09-27 words: 3186 flesch: 35 summary: The protocol and decisions made for each structure are based on our extensive experience in protein structure determination, 14-16 crystallographic software development, 17, 18 published guidelines on structure refinement and structure quality, 7, 19, 20 and previous campaigns of PDB structure re-refinement: 21,22 If raw diffraction data are available, the results of automatic processing of images by HKL-3000auto are examined to verify that the structure was determined in the correct space group and at optimal resolution. The website also serves as a repository for examined and, if found to be suboptimal, corrected versions of PDB structures of SARS-CoV-2 proteins and RNA fragments, with a focus on assessing the smallmolecule ligands modeled in those structures. keywords: data; density; diffraction; electron; models; pdb; protein; sars; structures cache: cord-283491-y6t64pux.txt plain text: cord-283491-y6t64pux.txt item: #44 of 69 id: cord-287450-hydy874v author: Wendt, K Ulrich title: Structures and diseases date: 2008 words: 2774 flesch: 30 summary: Starting the session on viral diseases, Rolf Hilgenfeld (University of Lübeck) reviewed the work from his laboratory on proteases of RNA viruses, such as severe acute respiratory syndrome (SARS) coronavirus and coxsackievirus B3, and also highlighted recent structural data on falcipain-2 from Plasmodium falciparum, discussing implications for the design of active-site directed and allosteric inhibitors for these cysteine proteases 14 . Ryota Kuroki (Japan Atomic Energy Agency) presented recent structural studies on the complex of human granulocyte colony-stimulating factor (GCSF), a cytokine used for treatment of granulopenia, with its receptor. keywords: binding; cell; complex; data; diseases; institute; molecular; protein; session; structure; university cache: cord-287450-hydy874v.txt plain text: cord-287450-hydy874v.txt item: #45 of 69 id: cord-292483-u0ycqelc author: Rossmann, Michael G. title: Future prospects date: 2011-04-16 words: 6489 flesch: 36 summary: In the past 2 or 3 years, cryo-EM has been able to produce, in favorable cases, three-dimensional images that are comparable to X-ray crystal structures of icosahedral viruses ( Jiang et al., 2008; Zhang et al., 2010) . Another use of cryo-EM structures can be to provide a low-resolution model for molecular replacement to initiate X-ray crystal structure determinations by means of phase extension, as was the case for a ribosomal subunit (Ban et al., 1998) or phiX174 virus particle (Dokland et al., 1998) . keywords: atomic; cryo; crystallography; data; electron; et al; microscopy; ray; resolution; structure; virus cache: cord-292483-u0ycqelc.txt plain text: cord-292483-u0ycqelc.txt item: #46 of 69 id: cord-292985-w62xaa4f author: Römer, Rudolf A. title: Flexibility and mobility of SARS-CoV-2-related protein structures date: 2020-07-12 words: 5209 flesch: 54 summary: Molecular dynamics simulations and multiple X-ray structure analyses Structures of Two Coronavirus Main Proteases: Implications for Substrate Binding and Antiviral Drug Design Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy Structure of M pro from COVID-19 virus and discovery of its inhibitors Importance of protein dynamics in the structure-based drug discovery of class A G protein-coupled receptors (GPCRs Protein conformational flexibility modulates kinetics and thermodynamics of drug binding Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses Protein flexibility and dynamics using constraint theory Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic Conformational change of proteins arising from normal mode calculations On the potential of normal mode analysis for solving difficult molecular replacement problems ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Normal mode analysis and applications in biological physics Constrained geometric simulation of diffusive motion in proteins Docking of Photosystem I Subunit C Using a Constrained Geometric Simulation Protein flexibility is key to cisplatin crosslinking in calmodulin Inhibition of HIV-1 protease: the rigidity perspective Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions The flexibility and dynamics of protein disulfide isomerase Something in the way she moves': We have downloaded protein structure files as deposited on the Protein Data Bank, 35 including all PDB codes that came up when using SARS-CoV-2 and Covid-19 as search terms, as well as minor variations in spelling. keywords: cluster; cov-2; cut; domain; flexibility; motion; protein; rigidity; sars; structure cache: cord-292985-w62xaa4f.txt plain text: cord-292985-w62xaa4f.txt item: #47 of 69 id: cord-301827-a7hnuxy5 author: Uversky, Vladimir N title: A decade and a half of protein intrinsic disorder: Biology still waits for physics date: 2013-04-29 words: 20990 flesch: 37 summary: Why these proteins are intrinsically disordered Caseins as rheomorphic proteins: interpretation of primary and secondary structures of the as1-, b-, and k-caseins The relation of polypeptide hormone structure and flexibility to receptor binding: the relevance of X-ray studies on insulins, glucagon and human placental lactogen High-resolution proton-magnetic-resonance studies of chromatin core particles Protein structure and enzyme activity Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded Protein structure protection commits gene expression patterns A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disorders Malleable machines take shape in eukaryotic transcriptional regulation Operational definition of intrinsically unstructured protein sequences based on susceptibility to the 20S proteasome Drugs for 'protein clouds': targeting intrinsically disordered transcription factors Protein dynamics: dancing on an ever-changing free energy stage Protein flexibility, not disorder, is intrinsic to molecular recognition TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder Intrinsic disorder and functional proteomics Sequence complexity of disordered protein Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization The protein non-folding problem: amino acid determinants of intrinsic order and disorder Composition Profiler: a tool for discovery and visualization of amino acid composition differences Comparing predictors of disordered protein A practical overview of protein disorder prediction methods Predicting protein disorder and induced folding: from theoretical principles to practical applications Prediction of protein disorder at the domain level Prediction of protein disorder Predicting intrinsic disorder in proteins: an overview Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins Intrinsic protein disorder in complete genomes Prediction and functional analysis of native disorder in proteins from the three kingdoms of life The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life Thousands of proteins likely to have long disordered regions Norton RS (2006) This study showed that the fraction of protein disorder was positively correlated with both measured RNA expression levels of E. coli genes in three different growth media and with predicted abundance levels of E. coli proteins. keywords: acid; amino; analysis; binding; cell; complex; diseases; disorder; disordered proteins; disordered regions; domains; evolution; fact; folding; function; idps; interactions; membrane; molten; p53; partners; protein structure; proteins; regions; regulation; residues; sequence; signaling; state; structure cache: cord-301827-a7hnuxy5.txt plain text: cord-301827-a7hnuxy5.txt item: #48 of 69 id: cord-304794-z2kx314h author: Métifiot, Mathieu title: G-quadruplexes in viruses: function and potential therapeutic applications date: 2014-11-10 words: 9130 flesch: 38 summary: Interestingly, TAg can unwind G4 DNA structures (122, 123) ; thus, it might play a crucial role in regulating replication as well as early and late transcription. Even if a 200-bp cis-regulatory element is necessary for efficient initiation, G4 structure formation at ORIs might be the key to selecting the firing origins (67, 68) . keywords: activity; binding; cells; dna; figure; formation; g4s; genome; human; promoter; protein; quadruplex; region; replication; rna; role; sequences; structures; transcription; viral; virus cache: cord-304794-z2kx314h.txt plain text: cord-304794-z2kx314h.txt item: #49 of 69 id: cord-310192-8x37nx4s author: Zhang, Huaqun title: Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy date: 2019-04-25 words: 7237 flesch: 29 summary: eLife, 3, e03678 NMR probing of invisible excited states using selectively labeled RNAs Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer Epigenetic regulation by long noncoding RNAs Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics Riboswitch structure in the ligand-free state Incorporation of isotopic, fluorescent, and heavy-atommodified nucleotides into RNAs by position-selective labeling of RNA Synthesis and applications of RNAs with positionselective labelling and mosaic composition Applications of PLOR in labeling large RNAs at specific sites Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations NMR detection of structures in the HIV-1 5 0 -leader RNA that regulate genome packaging Isotope labeling strategies for NMR studies of RNA Structure of HCV IRES domain II determined by NMR Structure determination of large biological RNAs Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: Comparison between uniformly and selectively 13 C labeled samples Accurate measurement of residual dipolar couplings in large RNAs by variable flip angle NMR Visualizing group II intron catalysis through the stages of splicing An introduction to biological NMR spectroscopy RNA structure analysis at single nucleotide resolution by selective 2 0 -hydroxyl acylation and primer extension (SHAPE) Speciation of a group I intron into a lariat capping ribozyme A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography Cryo EM structure of intact rotary H(+)-ATPase/synthase from Thermus thermophilus Multiple segmental and selective isotope labeling of large RNA for NMR structural studies Crystal structure of Pistol, a class of self-cleaving ribozyme RNA dynamics: Perspectives from spin labels Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies Cryo-EM: A unique tool for the visualization of macromolecular complexity Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy Metals induce transient folding and activation of the twister ribozyme RNA labeling, conjugation and ligation Chemical probes for higher-order structure in RNA NMR scaler couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation optimized spectroscopy Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands Group II intron self-splicing Structure of a group II intron in complex with its reverse transcriptase Three-state mechanism couples ligand and temperature sensing in riboswitches Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes RNA structure: Software for RNA secondary structure prediction and analysis Mapping the landscape of RNA dynamics with NMR spectroscopy Probing the structural dynamics of proteins and nucleic acids with optical tweezers Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM The structural and functional diversity of metabolite-binding riboswitches Synthesis and NMR of RNA with selective isotopic enrichment in the bases Preparation of specifically 2 H-and 13 C-labeled ribonucleotides Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension Crystal structure of the Varkud satellite ribozyme RNA structure through multidimensional chemical mapping Major groove width variations in RNA structures determined by NMR and impact of 13 C residual chemical shift anisotropy and 1 H-13 C residual dipolar coupling on refinement Crystal structure of a self-spliced group II intron Structural basis for exon recognition by a group II intron Preparation of large RNA oligonucleotides with complementary isotope-labeled segments for NMR structural studies NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: A primer NMR investigation of RNA structure Structure-activity relationship of flavin analogues that target the flavin mononucleotide riboswitch Single particle electron cryomicroscopy: Trends, issues and future perspective Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution A method for helical RNA global structure determination in solution using small-angle X-ray scattering and NMR measurements Principles for targeting RNA with drug-like small molecules Architecture and secondary structure of an entire HIV-1 RNA genome Advances in RNA structure analysis by chemical probing NMR of proteins and nucleic acids Determining RNA solution structure by segmental isotopic labeling and NMR: Application to Caenorhabditis elegans spliced leader RNA 1 Characterizing RNA excited states using NMR relaxation dispersion Nmr experiments for the measurement of carbon relaxation properties in highly enriched, uniformly 13 C, 15 N-labeled proteins-Application to 13 C(alpha) carbons MQ-HCN-based pulse sequences for the measurement of 13 C1'-1 H1 Structure of the 30 kDa HIV-1 RNA dimerization signal by a hybrid Cryo-EM, NMR, and molecular dynamics approach An excited state underlies gene regulation of a transcriptional riboswitch Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R (1rho) NMR spectroscopy Crystal structure of group II intron domain 1 reveals a template for RNA assembly Measurement of small scalar and dipolar couplings in purine and pyrimidine bases NMR studies of HAR1 RNA secondary structures reveal conformational dynamics in the human RNA DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy key: cord-310192-8x37nx4s authors: Zhang, Huaqun; Keane, Sarah C. title: Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy date: 2019-04-25 journal: keywords: analysis; approach; base; chemical; cryo; data; dynamics; et al; experiments; labeling; method; molecules; nmr; rna; rna structure; rnas; spectroscopy; structure; studies; study cache: cord-310192-8x37nx4s.txt plain text: cord-310192-8x37nx4s.txt item: #50 of 69 id: cord-310847-63gh2tg4 author: Uversky, Vladimir N title: The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins date: 2013-04-01 words: 19457 flesch: 42 summary: In fact, glutamic acid residue has a nonpolar surface of 69 Å 2 , and the estimated hydrophobic effect associated with the burial of this residue is 1.74 kcal/mol. + selectivity of Na,K-ATPase relies on the strategic positioning of glutamic acid residues. keywords: acid; acid residues; acidic; amino; amino acid; analysis; binding; cell; chain; channels; charge; disorder; domain; fact; function; glutamate; glutamic; glutamic acid; helix; human; idps; interactions; membrane; motif; pga; protein; region; repeat; residues; role; sequence; site; structure; terminal cache: cord-310847-63gh2tg4.txt plain text: cord-310847-63gh2tg4.txt item: #51 of 69 id: cord-312946-p2iazl7z author: Ziółkowska, Natasza E. title: Domain-Swapped Structure of the Potent Antiviral Protein Griffithsin and Its Mode of Carbohydrate Binding date: 2006-07-18 words: 6951 flesch: 48 summary: The structure of griffithsin was compared to the structures of a number of proteins that display a similar overall fold, including mannose binding lectins. Oligosaccharide and glycoprotein microarrays as tools in HIV glycobiology; glycan-dependent gp120/ protein interactions Characterization of jacalin, the human IgA and IgD binding lectin from jackfruit keywords: binding; carbohydrate; et al; griffithsin; lectins; mannose; protein; residues; site; structure cache: cord-312946-p2iazl7z.txt plain text: cord-312946-p2iazl7z.txt item: #52 of 69 id: cord-313694-p2sgaypq author: West, Christopher M. title: Current ideas on the significance of protein glycosylation date: 1986 words: 10925 flesch: 29 summary: The role of protein glycosylation in the compartmentalization and processing of mouse mammary tumor virus glycoproteins in mouse mammary tumor virus-infected rat hepatoma cells The formation of vesicular stomatitis virus (San Juan strain) becomes temperature-sensitive when glucose residues are retained on the oligosaccharides of the glycoprotein Deletions into a NI-I2-terrninal hydrophobic domain result in secretion of Rotavirus VP7, a resident endoplasmic reticulum membrane glycoprotein Glycoantigen expression is regulated both temporally and spatially during development in the cellular slime molds Dictyostelium discoideum and D. mucoroides The identification of N-linked oligosaccharides on the human CR2/Epstein-Barr virus receptor and their function in receptor metabolism, plasma membrane expression, and ligand binding Glycosylation and secretion of surfactant-associated glycoprotein A Complete glycosylation of the insulin and insulin-like growth factor 1 receptors is not necessary for their biosynthesis and function Chemistry, metabolism, and biological functions of sialic acids Effect of size and location of the oligosaccharide chain on protease degradation of bovine pancreatic ribonuclease Swainsonine inhibits glycoprotein degradation by isolated rat liver lysosomes Slime mold lectins Bacterial glycoconjugates are natural ligands for the carbohydrate binding site of discoidin I and influence its cellular compartmentalization Carbohydrate-specific receptors of the liver Hepatic clearance of serum glycoproteins The repair of the surface structure of animal cells Carbohydrate-mediated clearance of immune complexes from the circulation Carbohydrate-mediated clearance of antibody-antigen complexes from the circulation Surface carbohydrates and surface lectins are recognition determinants in phagocytosis The carbohydrate structure of porcine uteroferrin and the role of the high mannose chains in promoting uptake by the reticuloendothelial cells of the fetal liver Intracellular movement of cell surface receptors after endocytosis: resialylation of asialotransferrin receptor in human erythroleukemia cells Hyaluronic acid bonded to cell culture surfaces stimulated chondrogenesis in stage 24 limb mesenchyme cell cultures Lectin activation in Giardia lamblia by host protease: A novel hostparasite interaction Carbohydrates as recognition determinants in phagocytosis and in lectin-mediated killing of target cells Specificity of binding of a strain of uropathogenic Escherichia coli to Galcd-4Gal-containing glycosphingolipids Evidence for a malarial parasite interaction site on the major transmembrane protein of the human erythrocyte Adherent bacterial colonization in the pathogenesis of osteomyelitis Mucoproteins in relation to virus action The synthesis of complex carbohydrates by multiglycosyltransferase systems and their potential function in intercellular adhesion The receptor function of galactosyltransferase during cellular interactions The Biology of Glycoproteins A multivalent lacto-N-fucopentaose III-lysyllysine conjugate decompacts preimplantation mouse embryos, while the free oligosaccharide is ineffective Receptor function of mouse sperm surface galactosyltransferase during fertilization O-linked oligosaccharides of mouse egg ZP3 account for its sperm receptor activity Differential cell adhesion may result from nonspecific interactions between cell surface glycoproteins Specific alteration of N-CAM-mediated cell adhesion by an endoneuraminidase A heparin-bindifig domain from N-CAM is involved in neural cell-substratum adhesion Recognition of IgG by Fc receptor and complement: effects of glycosidase digestion Cell surface carbohydrates in cell recognition and response Feizi T: Cell interactions in preimplantation embryos: evidence for involvement of saccharides of the poly-Nacetyllactosamine series Mitochondrial synthesis of glycoproteins and surface properties of mitochondrial membranes Cell membranes in sponges The phosphomannosyl recognition system for intracellular and intercellular transport of lysosomal enzymes Cell-cell recognition in yeast, characterization of the sexual agglutination factors from Saccharomyces kluyveri Lymphocyte attachement to high endothelial venules during recirculation: a possible role for carbohydrates as recognition determinants Lymphocyte adhesion to immobolized polysaccharides suggests multiple carbohydrate receptors for recirculation Spontaneous glycosylation of glycosaminoglycan substrates by adherent fibroblasts Immunocytochemical demonstration of ecto-galactosyltransferase in absorptive intestinal cells Soluble lectins: a new class of extraeellular proteins Effect of choroquine on the degradation of L-fucose and the polypeptide moiety of plasma membrane glycoproteins Different half-lives of the carbohydrate and protein moieties of a 110000 dalton glycoprotein isolated from plasma membraned of rat liver Structural determinants of the capacity of heparin to inhibit the proliferation of vascular smooth muscle cells. This observation has led to the suggestion that cell surface carbohydrate might also establish a convection and diffusionqimited region around the cell in an area thick enough to be named, in certain cell types, the glycocalyx or fuzz. keywords: adhesion; binding; carbohydrate; cell; cell surface; function; glycoproteins; glycosylation; golgi; interactions; lysosomal; mannose; membrane; non; oligosaccharides; protein; receptor; recognition; role; structures; studies; surface cache: cord-313694-p2sgaypq.txt plain text: cord-313694-p2sgaypq.txt item: #53 of 69 id: cord-314321-klb8oe9q author: Chen, Serena H. title: Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date: 2020-04-18 words: 3176 flesch: 46 summary: Here, to obtain deeper insights into S protein structure for biological understanding and therapeutic targeting, we employ a combined molecular dynamics (MD) simulation and artificial intelligence (AI) methodology on a series of coronavirus S proteins. To better understand S protein structure keywords: coronavirus; cov-2; domain; fig; protein; protomer; sars; structures cache: cord-314321-klb8oe9q.txt plain text: cord-314321-klb8oe9q.txt item: #54 of 69 id: cord-314329-rzda8x62 author: Wells, Stephen A. title: Rigidity, normal modes and flexible motion of a SARS-CoV-2 (COVID-19) protease structure date: 2020-03-12 words: 4115 flesch: 46 summary: Protein structure is shown as spheres and coloured by amino acid type. Protein structure is shown as spheres and coloured by amino acid type. keywords: crystal; interactions; mode; motion; protease; protein; residues; site; structure cache: cord-314329-rzda8x62.txt plain text: cord-314329-rzda8x62.txt item: #55 of 69 id: cord-319906-s7kzp795 author: Zemla, Adam T title: StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase date: 2011-06-02 words: 7498 flesch: 35 summary: Twilight zone of protein sequence alignments Local alignment refinement using structural assessment Structural proteomics: a tool for genome annotation The structural alignment between two proteins: is there a unique answer Comparative analysis of protein structure alignments Flexible protein alignment and hinge detection Flexible structure alignment by chaining aligned fragment pairs allowing twists Matt: local flexibility aids protein multiple structure alignment Circular permutations of natural protein sequences: structural evidence Common structural cliques: a tool for protein structure and function analysis Connectivity independent protein-structure alignment: a hierarchical approach Topology independent protein structural alignment FlexSnap: Flexible non-sequential protein structure alignment Automated clustering of ensembles of alternative models in protein structure databases Iterative refinement of structure-based sequence alignments by seed extension LGA: a method for finding 3D similarities in protein structures STRALCP-structure alignment-based clustering of proteins A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features Structure of the RNA-dependent RNA polymerase of poliovirus A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design Oligomeric structures of poliovirus polymerase are important for function Clustered charged-to-alanine mutagenesis of poliovirus RNA-dependent RNA polymerase yields multiple temperature sensitive mutants defective in RNA synthesis Crystal structure of poliovirus 3CD protein: virally encoded protease and precursor to the RNA-dependent RNA polymerase Mutation of lysine residues in the nucleotide binding segments of the poliovirus RNA-dependent RNA polymerase Poliovirus RNA-dependent RNA polymerase (3Dpol): Structural, biochemical, and biological analysis of conserved structural motifs A and B Crystal structure of the RNA-dependent RNA polymerase form hepatitis C virus reveals a fully encircled active site Effects of mutations in poliovirus 3Dpol on RNA polymerase activity and on polyprotein cleavage SCOP: a structural classification of proteins database for the investigation of sequences and structures A mechanism for initiating RNA-dependent RNA polymerization Our StralSV algorithm detects structurally similar regions within a given pair of protein structures, and reports residue-residue correspondences only from those local regions that are contained within a larger, similar structural context. keywords: fragments; hits; polymerase; positions; protein; residue; rna; sequence; stralsv; structure; variability; window_size cache: cord-319906-s7kzp795.txt plain text: cord-319906-s7kzp795.txt item: #56 of 69 id: cord-322885-ob5euspo author: Durdagi, Serdar title: Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing date: 2020-09-09 words: 10828 flesch: 43 summary: These two highresolution SFX structures in different space groups reveal new active site residue conformations and intra-and inter-domain network and their dynamics at the atomic level, which helps us to better understand any related structural allosteric transitions of Mpro structure interacting with the inhibitors (Fig. 5 & figs. Additionally, Mpro structure bound to a non-covalent inhibitor (PDB ID: 6W63) in both monomeric and dimeric forms was utilized as target structure. keywords: 7cwc; binding; chain; coronavirus; cov-2; crystal; domain; drug; et al; fig; inhibitors; mpro; protease; protein; repurposing; residues; sars; sfx; simulations; site; space; structures; studies; temperature cache: cord-322885-ob5euspo.txt plain text: cord-322885-ob5euspo.txt item: #57 of 69 id: cord-324410-be2ith3z author: Wang, Qi title: Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry date: 2007-06-13 words: 3776 flesch: 42 summary: These results show that the influence of crystal packing or crystal environment on crystal structures of guest-host complexes is significant, which is consistent with the reported influence of crystal packing on protein structures To expand the application of the EUDOC program to supramolecular chemistry, we tested its ability to reproduce crystal structures of small-molecule complexes. keywords: complexes; crystal; crystal structures; eudoc; guest; host; program; structures cache: cord-324410-be2ith3z.txt plain text: cord-324410-be2ith3z.txt item: #58 of 69 id: cord-325328-3l3jznkj author: Holbrook, Stephen R title: RNA structure: the long and the short of it date: 2005-05-16 words: 3714 flesch: 38 summary: A database of non-canonical base pairs in RNA structures [30] , coupled with tools for the automatic identification and classification of RNA base pairs [31] , provides an initial description of RNA secondary structure. key: cord-325328-3l3jznkj authors: Holbrook, Stephen R title: RNA structure: the long and the short of it date: 2005-05-16 journal: Curr Opin Struct Biol DOI: 10.1016/j.sbi.2005.04.005 sha: doc_id: 325328 cord_uid: 3l3jznkj The database of RNA structure has grown tremendously since the crystal structure analyses of ribosomal subunits in 2000–2001. keywords: base; crystal; interaction; loops; motifs; ribosomal; rna; rnas; structure cache: cord-325328-3l3jznkj.txt plain text: cord-325328-3l3jznkj.txt item: #59 of 69 id: cord-329102-2y49kcwu author: Lan, Tammy C. T. title: Structure of the full SARS-CoV-2 RNA genome in infected cells date: 2020-06-30 words: 9327 flesch: 53 summary: Interactive drawing and editing of the RNA secondary structure Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond Simplified Estimation from Censored Normal Samples CONTRAfold: RNA secondary structure prediction without physics-based models Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1 MUSCLE: Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. keywords: base; cov-2; dms; et al; figure; fse; genome; rna; sars; sequence; stem; structure; î¼l cache: cord-329102-2y49kcwu.txt plain text: cord-329102-2y49kcwu.txt item: #60 of 69 id: cord-329504-91te3nu8 author: Croll, Tristan title: Making the invisible enemy visible date: 2020-10-07 words: 4827 flesch: 47 summary: Visualizing an unseen enemy; mobilizing structural biology to counter COVID-19 RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education Announcing the worldwide Protein Data Bank Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation AUSPEX: a graphical tool for X-ray diffraction data analysis The PDB_REDO Server for Macromolecular Structure Model Optimization Errors in protein structures This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. keywords: cov-2; data; errors; map; model; pdb; polymerase; protein; rna; sars; structures cache: cord-329504-91te3nu8.txt plain text: cord-329504-91te3nu8.txt item: #61 of 69 id: cord-330427-3eoio8uk author: Bassetto, Marcella title: Structural biology in antiviral drug discovery date: 2016-09-06 words: 4990 flesch: 26 summary: Furthermore, the numerous advances in science and technology promoted a faster and less expensive application of structural biology, increasing the speed of macromolecular structure determination, increasing the resolution of new crystal structures and allowing smaller amounts of protein and fewer crystals to be required to solve a structure [9] . One of the most recent applications of structural biology is crystallographic fragment screening Since 1934, when the first X-ray diffraction structure was reported for pepsin, this method emerged as an invaluable source of detailed and reliable information about protein structure, representing a significant step forward in comparison with previously used physical or chemical methods [2] . keywords: biology; crystal; discovery; drug; figure; identification; inhibitors; novel; structure; virus cache: cord-330427-3eoio8uk.txt plain text: cord-330427-3eoio8uk.txt item: #62 of 69 id: cord-330590-nu8ckeud author: Nieto-Rabiela, F. title: Viral metacommunities associated to bats and rodents at different spatial scales date: 2018-12-30 words: 4032 flesch: 30 summary: In general, it is more feasible to analyze the viral metacommunities associated with rodents at viral species scale by overlapping families, showing a weak phylogenetic signal between the host and the virus species. To measure the influence of the host phylogeny and functional characteristics of the host on viral community structure we hypothesized that both the expression of Clementsian structures based on the Niche Theory would prevail at different macroecological scales, and the host phylogeny will explain the viral metacommunity distribution as response of the shared host evolutionary histories and ecological relationships. keywords: clementsian; distribution; host; metacommunities; scale; species; structure; virus cache: cord-330590-nu8ckeud.txt plain text: cord-330590-nu8ckeud.txt item: #63 of 69 id: cord-340554-7cwp2xbw author: Yamasaki, Satoshi title: ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow date: 2019-03-06 words: 5383 flesch: 46 summary: Those small structural elements were derived from RNA structures found in the PDB. Rascal can predict tertiary structures with any secondary structures because the single stranded three-base fragments derived from RNA structures found in the PDB are not based on their secondary structure like RASSIE. keywords: acid; analysis; aptamer; complex; drugs; node; nucleic; prediction; protein; rascal; rna; simulations; structure; workflow cache: cord-340554-7cwp2xbw.txt plain text: cord-340554-7cwp2xbw.txt item: #64 of 69 id: cord-346546-yffwd0dc author: Douangamath, Alice title: Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date: 2020-05-27 words: 4101 flesch: 44 summary: Non-covalent fragments were soaked (Collins et al., 2017) , 123 whereas electrophile fragments were both soaked and co-crystallized as previously described 124 (Resnick et al., 2019) , to ensure that as many of the mass spectrometry hits as possible were 125 structurally observed. 615 MichelaNglo: sculpting protein views on web pages without coding An improved model for fragment-619 based lead generation at AstraZeneca Structure-based design,synthesis, and 622 biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors Conservation of substrate specificities among coronavirus main 625 proteases From SARS to MERS: crystallographic studies on coronaviral proteases 627 enable antiviral drug design Critical 629 assessment of important regions in the subunit association and catalytic action of the 630 severe acute respiratory syndrome coronavirus main protease Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like 634 protease cause different conformational changes in crystal structure Structure of M(pro) from SARS-CoV-2 and discovery of its 640 inhibitors Integration, scaling, space-group assignment and post-refinement. keywords: compounds; coronavirus; covalent; data; design; fragments; hits; inhibitors; protease; protein; sars; structure cache: cord-346546-yffwd0dc.txt plain text: cord-346546-yffwd0dc.txt item: #65 of 69 id: cord-346965-0oq2n0af author: Liu, Zhi-Ping title: Bridging protein local structures and protein functions date: 2008-04-18 words: 14492 flesch: 38 summary: Supplement 4: corrections and additions Kernel-based machine learning protocol for predicting DNA-binding proteins Inferring functional relationships of proteins from local sequence and spatial surface patterns CASTp: computed atlas of surface topography of proteins pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins Protein surface analysis for function annotation in high-throughput structural genomics pipeline Statistical analysis and prediction of protein-protein interfaces Flu virus proton channel analyzed: structures of key surface protein suggest different drug mechanisms Insights into protein-protein interfaces using a Bayesian network prediction method A tour of structural genomics Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces Identify catalytic triads of serine hydrolases by support vector machines The gene ontology annotation (GOA) database: sharing knowledge in Uniprot with gene ontology Ligand binding: functional site location, similarity and docking Predicting functionally important residues from sequence conservation Analysis and prediction of functionally important sites in proteins Prediction of interface residues in proteinprotein complexes by a consensus neural network method: test against NMR data Prediction of linear B-cell epitopes using amino acid pair antigenicity scale Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design Prediction of protein cellular attributes using pseudo amino acid composition (Erratum: ibid Structural bioinformatics and its impact to biomedical science A novel approach to predict active sites of enzyme molecules Predicting protein-protein interactions from sequences in a hybridization space MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM Recent progresses in protein subcellular location prediction Cell-PLoc: a package of web-servers for predicting subcellular localization of proteins in various organisms Prediction of protein structural classes Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS (Erratum: ibid High-throughput identification of interacting protein-protein binding sites Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families Predicting calciumbinding sites in proteins-a graph theory and geometry approach Practical limits of function prediction Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus Robust recognition of zinc binding sites in proteins Protein function in the post-genomic era Prediction of functionally important residues based solely on the computed energetics of protein structure Predicting DNA-binding proteins: approached from Chou's pseudo amino acid composition and other specific sequence features Prediction of protein-protein interaction sites in heterocomplexes with neural networks SURFACE: a database of protein surface regions for functional annotation Functional annotation by identification of local surface similarities: a novel tool for structural genomics HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces Using pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter Effective function annotation through catalytic residue conservation Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins Surprising similarities in structure comparison A method for localizing ligand binding pockets in protein structures SiteBase: a database for structurebased protein-ligand binding site comparison Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships Structural genomics: computational methods for structure analysis Exploiting 3D structural templates for detection of metal-binding sites in protein structures Uncovering network systems within protein structures Using a neural network and spatial clustering to predict the location of active sites in enzymes Distance-based identification of spatial motifs in proteins using constrained frequent subgraph mining LIGSITE csc : predicting ligand binding sites using the Connolly surface and degree of conservation LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins Protein structure comparison by alignment of distance matrices Mapping the protein universe An algorithm for predicting protein-protein interaction sites: abnormally exposed amino acid residues and secondary structure elements Global mapping of the protein structure space and application in structure-based inference of protein function Prediction of functional sites in proteins using conserved functional group analysis PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins PDBSite: a database of the 3D structure of protein functional sites A new bioinformatic approach to detect common 3D sites in protein structures Principles of protein-protein interactions Searching for functional sites in protein structures Protein-RNA interactions: a structural analysis Using electrostatic potentials to predict DNA-binding sites on DNAbinding proteins Quantitative assessment of relationship between sequence similarity and function similarity Shape variation in protein binding pockets and their ligands KEGG: An approach for clustering protein pockets into similar groups Analysis of protein surface patterns by pocket similarity network Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity An overview of the structures of protein-DNA complexes Amino acidbase interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level Protein-protein interaction: structurally conserved residues distinguish between binding sites and exposed protein surfaces A combined algorithm for genome-wide prediction of protein function Statistical models for discerning protein structures containing the DNA-binding helix-turn helix motif Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons SCOP: a structural classification of proteins database for the investigation of sequences and structures On the nature of cavities on protein surfaces: application to the identification of drug-binding sites ProMate: a structure based prediction program to identify the location of protein-protein binding sites Predicted protein-protein interaction sites from local sequence information CATH-a hierarchic classification of protein domain structures SSAP: sequential structure alignment program for protein structure comparison From protein structure to function Inference of protein function from protein structure Prediction of functional sites by analysis of sequence and structure conservation Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks Automatic prediction of protein function and detection of functional sites from structure The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data Molecular shape comparisons in searches for active sites and functional similarity Twilight zone of protein sequence alignments The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution A structural perspective on protein-protein interactions Computational methods of analysis of protein-protein interactions Integrating structure, bioinformatics, and enzymology to discover function-BioH, a new carboxylesterase from Escherichia coli A new method to detect related function among proteins independent of sequence and fold homology Structure and mechanism of the M2 proton channel of influenza A virus Predicting enzyme function from sequence: a systematic appraisal Network-based prediction of protein function EzyPred: a top-down approach for predicting enzyme functional classes and subclasses Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM PseAAC: a flexible web-server for generating various kinds of protein pseudo amino acid composition Using pseudo amino acid composition to predict protein subcellular location: approached with amino acid composition distribution Protein structure alignment by incremental combinatorial extension (CE) of the optimal path SiteEngines: recognition and comparison of binding sites and protein-protein interfaces Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity Hierarchical protein structure alignment using both secondary structure and atomic representations Identifying structural motifs in proteins Predicting metal-binding site residues in low-resolution structural models Annotation in three dimensions. keywords: acid; algorithm; amino; binding; dna; et al; features; functions; information; interaction; method; network; prediction; protein; protein function; protein structures; protein surface; residues; sequence; similarity; sites; structures; surface cache: cord-346965-0oq2n0af.txt plain text: cord-346965-0oq2n0af.txt item: #66 of 69 id: cord-349839-s32d3di2 author: Westhof, Eric title: RNA pseudoknots date: 1992-06-30 words: 3431 flesch: 53 summary: At the functional level, there is evidence that the realm of functions encompassed by RNA pseudoknots extends from the control of translation in prokaryotes, retroviruses and coronaviruses to the control of catalytic activity in ribozymes and the control of replication in some plant viruses. In an important piece of work, Pleij and his collaborators [2] demonstrated that because of the special geometry of RNA helices, it is possible for the two helical stems in the pseudoknot to be co-axially stacked. keywords: base; groove; helix; pseudoknot; rna; structure; trna cache: cord-349839-s32d3di2.txt plain text: cord-349839-s32d3di2.txt item: #67 of 69 id: cord-351222-9bfchw4u author: Rollinger, Judith M. title: Virtual screening for the discovery of bioactive natural products date: 2008 words: 10023 flesch: 34 summary: An idealized computer experiment SARS-CoV protease inhibitors design using virtual screening method from natural products libraries Sabadinine: a potential nonpeptide anti-severe acute-respiratory-syndrome agent identified using structure-aided design Identification of ellagic acid as potent inhibitor of protein kinase CK2: a successful example of a virtual screening application Structure-based virtual screening for plant-based ER -selective ligands as potential preventative therapy against age-related neuro-degenerative diseases Structure-based discovery of potassium channel blockers from natural products virtual screening and electrophysiological assay testing Pharmacophore modelling: applications in drug discovery Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B Rational selection of structurally diverse natural product scaffolds with favorable ADME properties for drug discovery Drugs? Some strategies and examples from literature combining virtual screening approaches and classical methods for activity exploitation are outlined below. keywords: activity; approach; authors; compounds; database; discovery; docking; drug; information; ligand; model; nps; pharmacophore; protein; screening; structure; target cache: cord-351222-9bfchw4u.txt plain text: cord-351222-9bfchw4u.txt item: #68 of 69 id: cord-354465-5nqrrnqr author: Haslinger, Christian title: RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties date: 1999 words: 10375 flesch: 61 summary: A new principle of RNA folding based on pseudoknotting Random induced subgraphs of generalized n-cubes Bio-molecular shapes and algebraic structures Generic properties of combinatory maps: Neural networks of RNA secondary structures Petersen family minors Sachs' linkless embedding conjecture Linear trees and RNA secondary structure How to search for RNA structures. Combinatorial aspects of RNA secondary structures have been studied in detail by Waterman and co-workers (Stein and Waterman, 1978; Waterman, 1978; Waterman and Smith, 1978a, b; Penner and Waterman, 1993; keywords: base; diagram; energy; graph; knots; neutral; number; pseudo; rna; sequences; structures; vertices cache: cord-354465-5nqrrnqr.txt plain text: cord-354465-5nqrrnqr.txt item: #69 of 69 id: cord-355327-d3gcfepx author: Fan, Samuel W title: Conformational changes in redox pairs of protein structures date: 2009-08-01 words: 9870 flesch: 41 summary: Emerging evidence supports the concept of two distinct types of disulfides in protein structures which have different functional roles. The Redox Pairs dataset contains 18,003 pairs of protein structures consisting of 4333 protein chains, of which 1238 (28.57%) are high-resolution structures (<2.2 Å). keywords: activity; binding; changes; cys; dataset; different; disorder; disulfide; group; morphing; pairs; proteins; redox; reduction; residues; sequence; sites; state; structure; transitions cache: cord-355327-d3gcfepx.txt plain text: cord-355327-d3gcfepx.txt