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blackbart protein [206 articles]

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  • The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant.
    Biophys J, Vol. 90, No. 10. (2006), pp. 3365-74.
    by B Ma, R Nussinov
    posted to acid amino amyloid beta-proteinchemistryultrastructure binding chemical complexeschemistryultrastructure computer dimerization drug fragmentschemistryultrastructure models molecular multiprotein mutation peptide protein simulation sites stability substitution by blackbart on 2007-04-20 21:18:20 as **
  • 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 **
  • Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35.
    Biophys J, Vol. 91, No. 3. (2006), pp. 824-33.
    by J Zheng, B Ma, CJ Tsai, R Nussinov
    posted to acid amino amyloidchemistry bonding cerevisiae cerevisiaemetabolism computer conformation dimerization homology hydrogen kinetics molecular mutation peptideschemistry prionschemistry protein proteinschemistry saccharomyces secondary sequence simulation structure by blackbart on 2007-04-20 21:18:20 as **
  • Potential folding-function interrelationship in proteins.
    Proteins, Vol. 56, No. 4. (2004), pp. 635-49.
    by A Barzilai, S Kumar, H Wolfson, R Nussinov
    posted to acidsphysiology amino biologymethodsstatistics computational conserved data databases design evolution folding models molecular numerical protein proteinschemistrymetabolismphysiology relationship research sequencephysiology structure-activity by blackbart on 2007-04-20 21:18:20 as **
  • How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding.
    J Mol Biol, Vol. 365, No. 1. (2007), pp. 257-73.
    by K Gunasekaran, R Nussinov
    posted to acidsanalysis amino binding conformation crystallography databases ligands protein proteinschemistry sites structure tertiary x-ray 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 **
  • Comparison of the human and worm p53 structures suggests a way for enhancing stability.
    Biochemistry, Vol. 45, No. 12. (2006), pp. 3925-33.
    by Y Pan, B Ma, AJ Levine, R Nussinov
    posted to animals caenorhabditis conformation eleganschemistry humans models molecular mutation p53chemistrygenetics protein suppressor tumor by blackbart on 2007-04-20 21:18:20 as **
  • Sequence and structure analysis of parallel beta helices: implication for constructing amyloid structural models.
    Structure, Vol. 14, No. 6. (2006), pp. 1059-72.
    by HH Tsai, K Gunasekaran, R Nussinov
    posted to acid acidschemistry amino amyloidchemistry animals data humans models molecular protein secondary sequence structural structure 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 **
  • Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families.
    Protein Sci, Vol. 15, No. 9. (2006), pp. 2120-8.
    by Del A Sol, H Fujihashi, D Amoros, R Nussinov
    posted to acid amino and binding data enzymeschemistry folding models molecular protein relationship sensitivity sequence sites specificity structure structure-activity tertiary by blackbart on 2007-04-20 21:18:20 as **
  • Temperature range of thermodynamic stability for the native state of reversible two-state proteins.
    Biochemistry, Vol. 42, No. 17. (2003), pp. 4864-73.
    by S Kumar, CJ Tsai, R Nussinov
    posted to archaeal binding coli conformation databases drug escherichia folding immunoglobulin lambda-chainschemistry models molecular protein proteinschemistry proteinschemistrymetabolism secondary sites stability structure sulfolobus temperature thermodynamics thioredoxinchemistry 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 **
  • Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4.
    J Am Chem Soc, Vol. 129, No. 6. (2007), pp. 1602-11.
    by D Fishelovitch, C Hazan, S Shaik, HJ Wolfson, R Nussinov
    posted to binding computer conformation cytochrome diazepamchemistrymetabolism enzyme humans models molecular p-450 protein quantum simulation sites systemchemistrymetabolism theory 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 **
  • A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core.
    J Mol Biol, Vol. 345, No. 5. (2005), pp. 1213-27.
    by N Haspel, D Zanuy, B Ma, H Wolfson, R Nussinov
    posted to acid acidschemistrygeneticsmetabolism amino amyloidchemistrymetabolism bonding calcitoninchemistrymetabolism computer electrostatics fragmentschemistrygeneticsmetabolism humans hydrogen hydrophobicity models molecular mutationgenetics peptide protein quaternary sequence simulation structure by blackbart on 2007-04-20 21:18:20 as **
  • Atomic-level description of amyloid beta-dimer formation.
    J Am Chem Soc, Vol. 128, No. 7. (2006), pp. 2158-9.
    by S Gnanakaran, R Nussinov, AE Garcia
    posted to amyloid beta-proteinchemistrymetabolism conformation dimerization models molecular protein quaternary structure thermodynamics by blackbart on 2007-04-20 21:18:20 as **
  • Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking.
    Structure, Vol. 12, No. 6. (2004), pp. 1027-38.
    by I Halperin, H Wolfson, R Nussinov
    posted to acid acidschemistry alaninechemistry amino animals binding conformation databases family glycinechemistry glycoproteinschemistry mice models molecular motifs multigene mutation protein thermodynamics 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 **
  • Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain.
    J Biol Chem, Vol. 279, No. 29. (2004), pp. 30523-30.
    by Y Pan, B Ma, O Keskin, R Nussinov
    posted to acid amino analysis antigens binding cd4chemistry computer conformation crystallography dna entropy envelope factors folding gp120chemistry hiv kinetics models molecular motifs mutation mutational protein secondary simulation sites software structure tertiary thermodynamics time x-ray by blackbart on 2007-04-20 21:18:19 as **
  • Structural basis for p53 binding-induced DNA bending.
    J Biol Chem, Vol. 282, No. 1. (2007), pp. 691-9.
    by Y Pan, R Nussinov
    posted to acid binding conformation dimerization dna-binding dnachemistry genes humans models molecular nucleic p53 p53metabolism protein proteinschemistry sites structure suppressor tertiary tumor by blackbart on 2007-04-20 21:18:19 as **
  • De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs.
    Structure, Vol. 14, No. 7. (2006), pp. 1137-48.
    by N Haspel, D Zanuy, C Aleman, H Wolfson, R Nussinov
    posted to acetyltransferaseschemistrygenetics acid amino coli data escherichia glycinechemistry models molecular motifsgenetics mutation nanostructureschemistry prolinechemistry protein proteinschemistrygenetics secondarygenetics sequence structure by blackbart on 2007-04-20 21:18:19 as **
  • Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues.
    Biochemistry, Vol. 46, No. 5. (2007), pp. 1205-18.
    by J Zheng, D Zanuy, N Haspel, CJ Tsai, C Aleman, R Nussinov
    posted to acidschemistry amino bonding engineeringmethods hydrogen hydrophobicity models molecular mutation nanostructures nanotubes protein proteinschemistry secondary structure by blackbart on 2007-04-20 21:18:19 as **
  • Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta(2)-microglobulin amyloidosis.
    Biochim Biophys Acta, Vol. 1753, No. 1. (2005), pp. 121-30.
    by H Benyamini, K Gunasekaran, H Wolfson, R Nussinov
    posted to 2-microglobulinchemistrymetabolism alignment amyloidbiosynthesis analysis beta humans models molecular protein secondary sequence structure by blackbart on 2007-04-20 21:18:19 as **
  • Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers.
    J Mol Biol, Vol. 341, No. 5. (2004), pp. 1327-41.
    by K Gunasekaran, CJ Tsai, R Nussinov
    posted to conformation macromolecular models molecular properties protein proteinschemistry substances subunitschemistrymetabolism surface thermodynamics by blackbart on 2007-04-20 21:18:19 as **
  • Insights into amyloid structural formation and assembly through computational approaches.
    Amyloid, Vol. 11, No. 3. (2004), pp. 143-61.
    by D Zanuy, K Gunasekaran, B Ma, HH Tsai, CJ Tsai, R Nussinov
    posted to amyloidchemistry animals biology computational folding humans models molecular protein secondary structure tertiary by blackbart on 2007-04-20 21:18:19 as **
  • The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29.
    J Mol Biol, Vol. 329, No. 3. (2003), pp. 565-84.
    by D Zanuy, R Nussinov
    posted to acid amino amyloidchemistry binding bonding fragmentschemistry humans hydrogen hydrophobicity models molecular peptide protein quaternary relationship sequence structure structure-activity thermodynamics 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 **
  • Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface.
    Proc Natl Acad Sci U S A, Vol. 102, No. 11. (2005), pp. 3988-93.
    by B Ma, Y Pan, K Gunasekaran, RB Venkataraghavan, AJ Levine, R Nussinov
    posted to acid amino computer crystallography dimerization dnachemistrymetabolism factors motifs p53chemistrymetabolism protein simulation software structure suppressor tertiary time tumor 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 **
  • The stability and dynamics of the human calcitonin amyloid peptide DFNKF.
    Biophys J, Vol. 87, No. 1. (2004), pp. 146-58.
    by HH Tsai, D Zanuy, N Haspel, K Gunasekaran, B Ma, CJ Tsai, R Nussinov
    posted to amyloidchemistry calcitoninchemistry computer conformation dimerization humans hydrophobicity models molecular peptideschemistry protein secondary simulation structure 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 **
  • FlexProt: alignment of flexible protein structures without a predefinition of hinge regions.
    J Comput Biol, Vol. 11, No. 1. (2004), pp. 83-106.
    by M Shatsky, R Nussinov, HJ Wolfson
    posted to alignment analysis biologymethods computational computer models molecular protein sequence simulation software structure tertiary 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 **
  • Residues crucial for maintaining short paths in network communication mediate signaling in proteins.
    Mol Syst Biol, Vol. 2 (2006)
    by Del A Sol, H Fujihashi, D Amoros, R Nussinov
    posted to acids allosteric amino conformation conserved folding protein proteinschemistryphysiology regulation sequence 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 **
  • "Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains.
    Structure, Vol. 14, No. 12. (2006), pp. 1811-21.
    by J Liu, Y Pan, B Ma, R Nussinov
    posted to acid amino and binding brca1 computer data humans interaction intracellular mappingmethods models molecular mutation p53chemistry peptides phosphoproteinschemistry protein proteinchemistry proteinschemistry secondary sequence signaling simulation sites structure suppressor tertiary thermodynamics tumor 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 **
  • In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1.
    Biochemistry, Vol. 44, No. 5. (2005), pp. 1423-32.
    by Y Pan, B Ma, RB Venkataraghavan, AJ Levine, R Nussinov
    posted to acid amino biologymethods bonding computational computer conformation cysteinegenetics humans hydrogen methioninegenetics models molecular mutagenesis neoplasm p53chemistrygenetics prolinegenetics protein proteinschemistrygenetics secondarygenetics serinegenetics simulation site-directed structure substitutiongenetics suppressor thermodynamics tumor 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 **
  • SiteEngines: recognition and comparison of binding sites and protein-protein interfaces.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (2005), pp. W337-41.
    by Shulman A Peleg, R Nussinov, HJ Wolfson
    posted to acidschemistry amino binding complexeschemistrymetabolism conformation interaction interface internet mappingmethods multiprotein protein sites software user-computer 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 **
  • CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible.
    J Mol Biol, Vol. 350, No. 3. (2005), pp. 514-27.
    by Y Pan, B Ma, R Nussinov
    posted to acid amino antigens binding bonding cd4metabolismphysiology computer conformation crystallography databases envelope factors folding gp120chemistrymetabolism hiv hiv-1metabolism hydrogen ligands models molecular motifs protein secondary simulation structure tertiary thermodynamics time x-ray by blackbart on 2007-04-20 21:18:18 as **
  • Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences.
    Protein Sci, Vol. 12, No. 9. (2003), pp. 1882-93.
    by B Ma, R Nussinov
    posted to acid amino bonding conformation data entropy folding homology hydrogen isoforms models molecular nerve peptideschemistry protein proteinschemistry secondary sequence software statistical structure tertiary thermodynamics tissue 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