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blackbart algorithms [59 articles]

Recent papers added to blackbart library classified by the tag algorithms. You can also see everyone's algorithms.
  • Recognition of functional sites in protein structures.
    J Mol Biol, Vol. 339, No. 3. (2004), pp. 607-33.
    by Shulman A Peleg, R Nussinov, HJ Wolfson
    posted to algorithms bonding catalytic conformation domain hydrogen models molecular protein proteinschemistry by blackbart on 2007-04-20 21:18:20 as **
  • Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design.
    Curr Med Chem, Vol. 11, No. 1. (2004), pp. 71-90.
    by O Dror, Shulman A Peleg, R Nussinov, HJ Wolfson
    posted to algorithms binding computer-aided conformation databases design drug drugchemistry factual interactions ligands molecular protein quantitative receptors relationship structure-activity by blackbart on 2007-04-20 21:18:20 as **
  • MASS: multiple structural alignment by secondary structures.
    Bioinformatics, Vol. 19 Suppl 1 (2003), pp. i95-104.
    by O Dror, H Benyamini, R Nussinov, H Wolfson
    posted to acid algorithms alignmentmethods amino analysis conformation data homology interface models molecular motifs protein proteinmethods proteinschemistry secondary sequence software structure tertiary user-computer by blackbart on 2007-04-20 21:18:20 as **
  • Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder.
    Proc Natl Acad Sci U S A, Vol. 102, No. 23. (2005), pp. 8174-9.
    by HH Tsai, M Reches, CJ Tsai, K Gunasekaran, E Gazit, R Nussinov
    posted to acid algorithms amino amyloidchemistry asparaginechemistry bonding computer humans hydrogen mutationgenetics peptideschemistrygenetics protein quaternary secondary sequence simulation structure temperature thermodynamics by blackbart on 2007-04-20 21:18:20 as **
  • A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.
    Bioinformatics, Vol. 22, No. 11. (2006), pp. 1343-52.
    by G Wainreb, N Haspel, HJ Wolfson, R Nussinov
    posted to acid algorithms amino analysis animals biologymethods cluster computational conformation data homology humans models molecular protein proteinschemistry secondary sequence software structure by blackbart on 2007-04-20 21:18:20 as **
  • Multiple structural alignment by secondary structures: algorithm and applications.
    Protein Sci, Vol. 12, No. 11. (2003), pp. 2492-507.
    by O Dror, H Benyamini, R Nussinov, HJ Wolfson
    posted to algorithms alignmentmethods binding conformation dnachemistry folding models molecular protein proteinschemistry sequence sites structure tertiary by blackbart on 2007-04-20 21:18:20 as **
  • Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking.
    Curr Med Chem, Vol. 11, No. 1. (2004), pp. 91-107.
    by Schneidman D Duhovny, R Nussinov, HJ Wolfson
    posted to algorithms computer-aided conformation databases design drug drugchemistry factual ligands protein proteinschemistry quantitative receptors relationship structure-activity by blackbart on 2007-04-20 21:18:19 as **
  • Geometry-based flexible and symmetric protein docking.
    Proteins, Vol. 60, No. 2. (2005), pp. 224-31.
    by Schneidman D Duhovny, Y Inbar, R Nussinov, HJ Wolfson
    posted to algorithms animals biologymethods computational computer conformation databases dimerization electrostatics folding homology humans interaction internet macromolecular mappingmethods models molecular mutation of protein proteomicsmethods reproducibility results simulation software statistical structural structure substances tertiary by blackbart on 2007-04-20 21:18:19 as **
  • EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.
    Acta Crystallogr D Biol Crystallogr, Vol. 63, No. Pt 1. (2007), pp. 42-9.
    by O Dror, K Lasker, R Nussinov, H Wolfson
    posted to algorithms conformation cryoelectron data folding groel interpretation macromolecular microscopymethods models molecular protein proteinchemistry secondary software statistical structure substances tertiary by blackbart on 2007-04-20 21:18:19 as **
  • Reducing the computational complexity of protein folding via fragment folding and assembly.
    Protein Sci, Vol. 12, No. 6. (2003), pp. 1177-87.
    by N Haspel, CJ Tsai, H Wolfson, R Nussinov
    posted to acid acidschemistry algorithms alignmentmethods amino analysis biologymethods cluster computational conformation data databases folding fragmentschemistry models molecular peptide protein sequence by blackbart on 2007-04-20 21:18:19 as **
  • Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking.
    Proteins, Vol. 52, No. 1. (2003), pp. 107-12.
    by Schneidman D Duhovny, Y Inbar, V Polak, M Shatsky, I Halperin, H Benyamini, A Barzilai, O Dror, N Haspel, R Nussinov, HJ Wolfson
    posted to algorithms alpha-amylasechemistrymetabolism alpha-betachemistrymetabolism antibodieschemistryimmunology antigen antigens bacterial binding capsid exotoxinschemistrymetabolism glycoproteins hemagglutinin influenza interaction kinaseschemistrymetabolism macromolecular mapping membrane models molecular phosphoenolpyruvate phosphotransferase protein protein-serine-threonine proteinschemistryimmunology proteinschemistrymetabolism receptors sites substances sugar systemchemistrymetabolism t-cell viral viruschemistryimmunology by blackbart on 2007-04-20 21:18:19 as **
  • Hierarchical protein folding pathways: a computational study of protein fragments.
    Proteins, Vol. 51, No. 2. (2003), pp. 203-15.
    by N Haspel, CJ Tsai, H Wolfson, R Nussinov
    posted to acid algorithms alignmentmethods amino conformation data databases folding homology molecular protein proteinschemistrygenetics secondary sequence structure by blackbart on 2007-04-20 21:18:19 as **
  • A hierarchical protein folding scheme based on the building block folding model.
    Methods Mol Biol, Vol. 350 (2007), pp. 189-204.
    by N Haspel, G Wainreb, Y Inbar, HH Tsai, CJ Tsai, HJ Wolfson, R Nussinov
    posted to algorithms chemical conformation folding models molecular protein proteinschemistry by blackbart on 2007-04-20 21:18:19 as **
  • A method for simultaneous alignment of multiple protein structures.
    Proteins, Vol. 56, No. 1. (2004), pp. 143-56.
    by M Shatsky, R Nussinov, HJ Wolfson
    posted to algorithms alignmentmethods binding biologymethods chains computational databases enzymeschemistry globinschemistry gtp-binding heterotrimeric lectinschemistry markov models molecular phosphotyrosinemetabolism protein proteinschemistry proteinschemistryclassificationmetabolism secondary sequence sites software structure tertiary by blackbart on 2007-04-20 21:18:18 as **
  • From structure to function: methods and applications.
    Curr Protein Pept Sci, Vol. 6, No. 2. (2005), pp. 171-83.
    by HJ Wolfson, M Shatsky, Schneidman D Duhovny, O Dror, Shulman A Peleg, B Ma, R Nussinov
    posted to algorithms alignment biology computational computer conformation forecasting humans models molecular protein proteinschemistrymetabolism relationship sequence simulation structure-activity by blackbart on 2007-04-20 21:18:18 as **
  • Approaching the CAPRI challenge with an efficient geometry-based docking.
    Proteins, Vol. 60, No. 2. (2005), pp. 217-23.
    by Y Inbar, Schneidman D Duhovny, I Halperin, A Oron, R Nussinov, HJ Wolfson
    posted to algorithms biologymethods computational computer conformation crystallography databases dimerization electrostatics folding homology interaction internet macromolecular mappingmethods models molecular mutation of protein proteomicsmethods reproducibility results simulation software statistical structural structure substances tertiary theoretical x-ray by blackbart on 2007-04-20 21:18:18 as **
  • SiteLight: binding-site prediction using phage display libraries.
    Protein Sci, Vol. 12, No. 7. (2003), pp. 1344-59.
    by I Halperin, H Wolfson, R Nussinov
    posted to algorithms animals bacteriophageschemistrygenetics binding carrier chemistry combinatorial conformation databases dna-binding factors fragmentschemistryisolation fusion heat-shock hsc70 hsp70 humans library of peptide protein proteins proteinschemistry proteinschemistryclassificationgenetics proteinschemistrygenetics purification recombinant reproducibility results sites techniques transcription by blackbart on 2007-04-20 21:18:18 as **
  • EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 1. (2007), pp. 28-39.
    by K Lasker, O Dror, M Shatsky, R Nussinov, HJ Wolfson
    posted to 2chemistryultrastructure adaptor algorithms biologymethods center complex computational computer-assistedmethods cryoelectron databases groel homology image isomerasechemistryultrastructure microscopymethods models molecular photosynthetic processing protein proteinchemistryultrastructure proteinschemistryultrastructure reaction secondary structural structure tertiary triose-phosphate by blackbart on 2007-04-20 21:18:18 as **
  • PRISM: protein interactions by structural matching.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (2005), pp. W331-6.
    by U Ogmen, O Keskin, AS Aytuna, R Nussinov, A Gursoy
    posted to algorithms conformation interaction interface internet mappingmethods protein software user-computer by blackbart on 2007-04-20 21:18:18 as **
  • The multiple common point set problem and its application to molecule binding pattern detection.
    J Comput Biol, Vol. 13, No. 2. (2006), pp. 407-28.
    by M Shatsky, Shulman A Peleg, R Nussinov, HJ Wolfson
    posted to adenosine algorithms binding catalytic conformation domain estradiolmetabolism kinaseschemistrymetabolism ligands models molecular protein proteinschemistrymetabolism sites triphosphatemetabolism by blackbart on 2007-04-20 21:18:18 as **
  • Prediction of multimolecular assemblies by multiple docking.
    J Mol Biol, Vol. 349, No. 2. (2005), pp. 435-47.
    by Y Inbar, H Benyamini, R Nussinov, HJ Wolfson
    posted to algorithms antigen antigens b bchemistrymetabolism binding biology class computational cytoskeletal factorschemistry folding histocompatibility i-kappa iichemistry kinase kinaseschemistrymetabolism models molecular nf-kappa polymerase protein protein-serine-threonine proteinschemistry proteinschemistrymetabolism quaternary receptors rna structure suppressor t-cellchemistry transcription tumor by blackbart on 2007-04-20 21:18:18 as **
  • Protein structure prediction via combinatorial assembly of sub-structural units.
    Bioinformatics, Vol. 19 Suppl 1 (2003), pp. i158-68.
    by Y Inbar, H Benyamini, R Nussinov, HJ Wolfson
    posted to acid algorithms alignmentmethods amino analysis and binding chemical chemistry combinatorial computer conformation glucosyltransferaseschemistry homology models molecular of protein proteinmethods proteinschemistry reproducibility results sensitivity sequence simulation sites specificity structure subunits techniquesmethods tertiary by blackbart on 2007-04-20 21:18:17 as **
  • BioInfo3D: a suite of tools for structural bioinformatics.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (2004), pp. W503-7.
    by M Shatsky, O Dror, Schneidman D Duhovny, R Nussinov, HJ Wolfson
    posted to algorithms biology computational conformation internet ligands macromolecular protein proteinschemistrymetabolism secondary software structure substances by blackbart on 2007-04-20 21:18:17 as **
  • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.
    Protein Sci, Vol. 13, No. 4. (2004), pp. 1043-55.
    by O Keskin, CJ Tsai, H Wolfson, R Nussinov
    posted to algorithms analysis binding biology cluster computational databases factual folding models molecular properties protein proteinschemistry sites structure surface tertiary by blackbart on 2007-04-20 21:18:17 as **
  • PatchDock and SymmDock: servers for rigid and symmetric docking.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (2005), pp. W363-7.
    by Schneidman D Duhovny, Y Inbar, R Nussinov, HJ Wolfson
    posted to algorithms complexeschemistry conformation interface internet ligands multiprotein protein software user-computer by blackbart on 2007-04-20 21:18:17 as **
  • Conservation and amyloid formation: a study of the gelsolin-like family.
    Proteins, Vol. 51, No. 2. (2003), pp. 266-82.
    by H Benyamini, K Gunasekaran, H Wolfson, R Nussinov
    posted to acid actin algorithms alignment amino amyloidchemistrygeneticsmetabolism conserved databases depolymerizing factors gelsolinchemistrygeneticsmetabolism glycinechemistrygenetics hydrophobicity microfilament protein proteinschemistrygeneticsmetabolism secondary sequence sequencegenetics structure tertiary by blackbart on 2007-04-20 21:18:17 as **
  • Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways.
    Protein Eng Des Sel, Vol. 18, No. 1. (2005), pp. 11-24.
    by O Keskin, R Nussinov
    posted to algorithms models molecular proteinschemistryphysiology relationship structure-activity by blackbart on 2007-04-20 21:18:17 as **
  • Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation.
    Proteins, Vol. 42, No. 2. (2001), pp. 279-93.
    by AI Su, DM Lorber, GS Weston, WA Baase, BW Matthews, BK Shoichet
    posted to algorithms and binding biologymethods computational databases dehydrogenasechemistry enzyme factual information inhibitorschemistry ligands retrieval sites storage synthaseantagonists tetrahydrofolate thymidylate bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Protein docking and complementarity.
    J Mol Biol, Vol. 221, No. 1. (1991), pp. 327-46.
    by BK Shoichet, ID Kuntz
    posted to algorithms chymotrypsinchemistry computer conformation endopeptidaseschemistry inhibitorschemistry models molecular protease protein proteinschemistry simulation subtilisinschemistry bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Testing a flexible-receptor docking algorithm in a model binding site.
    J Mol Biol, Vol. 337, No. 5. (2004), pp. 1161-82.
    by BQ Wei, LH Weaver, AM Ferrari, BW Matthews, BK Shoichet
    posted to algorithms bacteriophage binding computer crystallography databases factual ligands models molecular muramidasechemistry pliability protein simulation sites t4enzymology x-ray bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • A model binding site for testing scoring functions in molecular docking.
    J Mol Biol, Vol. 322, No. 2. (2002), pp. 339-55.
    by BQ Wei, WA Baase, LH Weaver, BW Matthews, BK Shoichet
    posted to acid algorithms amino bacteriophage binding calorimetry conformation crystallography databases factual hydrophobicity ligands models molecular muramidasechemistrygeneticsmetabolism mutation protein sites software substitution t4chemistry x-ray bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Matching chemistry and shape in molecular docking.
    Protein Eng, Vol. 6, No. 7. (1993), pp. 723-32.
    by BK Shoichet, ID Kuntz
    posted to algorithms aprotininchemistrymetabolism binding chemistry computer crystallization dehydrogenasechemistrymetabolism deoxyuracil design drug electrochemistry ligands methotrexatechemistrymetabolism nucleotideschemistrymetabolism physical simulation sites synthasechemistrymetabolism tetrahydrofolate thymidylate trypsinchemistrymetabolism bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Decoys for docking.
    J Med Chem, Vol. 48, No. 11. (2005), pp. 3714-28.
    by AP Graves, R Brenk, BK Shoichet
    posted to acetylcholinesterasechemistry algorithms binding dehydrogenasechemistry ligands models molecular phosphorylasechemistry protein purine-nucleoside quantitative relationship sites structure-activity synthasechemistry tetrahydrofolate thrombinchemistry thymidylate bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Predicting substrates by docking high-energy intermediates to enzyme structures.
    J Am Chem Soc, Vol. 128, No. 49. (2006), pp. 15882-91.
    by JC Hermann, E Ghanem, Y Li, FM Raushel, JJ Irwin, BK Shoichet
    posted to algorithms amidohydrolaseschemistrymetabolism binding chemical computer crystallography databases hydrolaseschemistrymetabolism models phosphoric protein simulation sites specificity stereoisomerism substrate triester x-ray bibtex-import by blackbart on 2007-04-20 21:16:34 as **
  • Flexible ligand docking using conformational ensembles.
    Protein Sci, Vol. 7, No. 4. (1998), pp. 938-50.
    by DM Lorber, BK Shoichet
    posted to algorithms binding bindingphysiology computer conformation crystallography databases deoxyuracil design drug ligands methotrexatechemistry models molecular nadchemistry nucleotideschemistry protein proteinschemistry simulation sitesphysiology software structure x-ray bibtex-import by blackbart on 2007-04-20 21:16:33 as **
  • Predicting the structure of protein complexes: a step in the right direction.
    Chem Biol, Vol. 3, No. 3. (1996), pp. 151-6.
    by BK Shoichet, ID Kuntz
    posted to algorithms conformation models molecular protein bibtex-import by blackbart on 2007-04-20 21:16:32 as **
  • A method to determine the filter matrix in four-dye fluorescence-based DNA sequencing.
    Electrophoresis, Vol. 18, No. 1. (1997), pp. 23-5.
    by W Huang, Z Yin, DR Fuhrmann, DJ States, LJ Thomas
    posted to algorithms analysis dnamethods dyes fluorescent mathematics sequence bibtex-import by blackbart on 2007-04-20 21:15:04 as **
  • SAGA: a subgraph matching tool for biological graphs.
    Bioinformatics, Vol. 23, No. 2. (2007), pp. 232-9.
    by Y Tian, RC Mceachin, C Santos, DJ States, JM Patel
    posted to algorithms automatedmethods biological computer database databases graphics interface management models pattern protein proteomemetabolism recognition signal simulation software systems transductionphysiology user-computer bibtex-import by blackbart on 2007-04-20 21:15:04 as **
  • Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.
    Proteomics, Vol. 5, No. 13. (2005), pp. 3246-61.
    by M Adamski, T Blackwell, R Menon, L Martens, H Hermjakob, C Taylor, GS Omenn, DJ States
    posted to algorithms blood cooperation databases desorption-ionization distribution false humans international laser mass matrix-assisted models peptideschemistry pilot poisson positive projects protein proteinschemistry proteomechemistry proteomicsmethods reactions reference spectrometry statistical values bibtex-import by blackbart on 2007-04-20 21:15:04 as **
  • Sequence assembly validation by multiple restriction digest fragment coverage analysis.
    Proc Int Conf Intell Syst Mol Biol, Vol. 6 (1998), pp. 140-7.
    by EC Rouchka, DJ States
    posted to algorithms alignmentmethodsstatistics analysis artificial base data dna dnagenetics dnamethodsstatistics fingerprinting intelligence mappingmethodsstatistics numerical of reproducibility restriction results sequence bibtex-import by blackbart on 2007-04-20 21:15:04 as **
  • Lane tracking software for four-color fluorescence-based electrophoretic gel images.
    Genome Res, Vol. 6, No. 11. (1996), pp. 1110-7.
    by ML Cooper, DR Maffitt, JD Parsons, L Hillier, DJ States
    posted to algorithms analysismethods electrophoresis fluorescence gelmethods polyacrylamide sequence software statistics bibtex-import by blackbart on 2007-04-20 21:15:04 as **
  • Computationally efficient cluster representation in molecular sequence megaclassification.
    Proc Int Conf Intell Syst Mol Biol, Vol. 1 (1993), pp. 387-94.
    by DJ States, NL Harris, L Hunter
    posted to algorithms analysis analysismethods cluster coli computing design escherichia mathematical of proteins proteinsclassification reproducibility results ribosomal sequence software bibtex-import by blackbart on 2007-04-20 21:15:04 as **
  • Molecular sequence accuracy and the analysis of protein coding regions.
    Proc Natl Acad Sci U S A, Vol. 88, No. 13. (1991), pp. 5518-22.
    by DJ States, D Botstein
    posted to acid algorithms amino animals base bayes cerevisiaegenetics codon elastasegenetics homology humans neutrophilsenzymology nucleic pancreatic saccharomyces schistosomaenzymology sequence theorem trypsingenetics bibtex-import by blackbart on 2007-04-20 21:15:04 as **
  • Combined use of sequence similarity and codon bias for coding region identification.
    J Comput Biol, Vol. 1, No. 1. (1994), pp. 39-50.
    by DJ States, W Gish
    posted to acid algorithms amino analysis animals bacillus base cerevisiae codon coli data databases dnamethods drosophila escherichia factual homology humans melanogaster molecular nucleic saccharomyces schizosaccharomyces sequence software subtilis bibtex-import by blackbart on 2007-04-20 21:15:03 as **
  • Bioinformatics code must enforce citation.
    Nature, Vol. 417, No. 6889. (2002)
    by DJ States
    posted to algorithms and authorship biologymanpowermethodsstandards computational databases geneticstandards information interface internetstandards peer plagiarism publishingstandards research retrievalstandards review softwarestandards storage user-computer bibtex-import by blackbart on 2007-04-20 21:15:02 as **
  • Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.
    Proteomics, Vol. 5, No. 13. (2005), pp. 3226-45.
    by GS Omenn, DJ States, M Adamski, TW Blackwell, R Menon, H Hermjakob, R Apweiler, BB Haab, RJ Simpson, JS Eddes, EA Kapp, RL Moritz, DW Chan, AJ Rai, A Admon, R Aebersold, J Eng, WS Hancock, SA Hefta, H Meyer, YK Paik, JS Yoo, P Ping, J Pounds, J Adkins, X Qian, R Wang, V Wasinger, CY Wu, X Zhao, R Zeng, A Archakov, A Tsugita, I Beer, A Pandey, M Pisano, P Andrews, H Tammen, DW Speicher, SM Hanash
    posted to acidchemistrypharmacology acidpharmacology algorithms anticoagulantspharmacology biology blood citric computational databases desorption-ionization dnachemistry edetic frames heparinchemistry humans immunoassay laser mass matrix-assisted open pilot projects protein proteinschemistry proteomicsmethods reading spectrometry spectrometrymethods bibtex-import by blackbart on 2007-04-20 21:15:01 as **