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blackbart conformation [148 articles]

最近 blackbart さんのライブラリに追加された論文の中から タグ conformation. You can also see everyone's conformation.
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • Structure by design: from single proteins and their building blocks to nanostructures.
    Trends Biotechnol, Vol. 24, No. 10. (2006), pp. 449-54.
    by CJ Tsai, J Zheng, C Aleman, R Nussinov
    posted to carbonchemistryultrastructure chemical conformation design drug models nanotechnologymethods nanotubes peptidechemistryultrastructure protein subunitschemical synthesis by blackbart on 2007-04-20 21:18:18 as **
  • Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes.
    J Biol Chem, Vol. 279, No. 51. (2004), pp. 53875-85.
    by B Ma, R Nussinov
    posted to acid amino animals conformation conserved cryoelectron crystallography data electrostatics elongation factor factorschemistryphysiology histidinechemistry homology humans microscopy models molecular motifs peptide peptideschemistry protein proteinschemistry ribosomeschemistry rna secondary sequence software species specificity statistical structure termination tertiary thermodynamics transferchemistry tuchemistry x-ray 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 **
  • Beta2-microglobulin amyloidosis: insights from conservation analysis and fibril modelling by protein docking techniques.
    J Mol Biol, Vol. 330, No. 1. (2003), pp. 159-74.
    by H Benyamini, K Gunasekaran, H Wolfson, R Nussinov
    posted to 2-microglobulinchemistrymetabolism acid alignmentmethods amino amyloidosis beta bindingphysiology computer conformation conserved denaturation disulfideschemistry familialmetabolismphysiopathology humans models molecular protein sequence simulation ureachemistry by blackbart on 2007-04-20 21:18:18 as **
  • Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants.
    Protein Eng, Vol. 16, No. 8. (2003), pp. 561-75.
    by B Ma, R Nussinov
    posted to 2-microglobulinchemistrygenetics amyloidosisetiology beta computer conformation denaturation genetics humans models molecular motion pliability protein secondary simulation solubility structure temperature variation by blackbart on 2007-04-20 21:18:18 as **
  • Simulations as analytical tools to understand protein aggregation and predict amyloid conformation.
    Curr Opin Chem Biol, Vol. 10, No. 5. (2006), pp. 445-52.
    by B Ma, R Nussinov
    posted to amyloidchemistry computer conformation hydrophobicity models molecular of predictive protein simulation tests value by blackbart on 2007-04-20 21:18:17 as **
  • Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I.
    Biochemistry, Vol. 42, No. 13. (2003), pp. 3674-87.
    by K Gunasekaran, B Ma, B Ramakrishnan, PK Qasba, R Nussinov
    posted to acid amino animals binding catalytic cattle computer conformation conserved crystallization crystallography data diphosphate domain galactosemetabolism galactosyltransferaseschemistryphysiology homology kinetics models molecular protein sequence sequencegenetics simulation sites tryptophangeneticsmetabolism uridine x-ray by blackbart on 2007-04-20 21:18:17 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 **
  • Designing a nanotube using naturally occurring protein building blocks.
    PLoS Comput Biol, Vol. 2, No. 4. (2006)
    by CJ Tsai, J Zheng, R Nussinov
    posted to conformation hiv-1chemistry models molecular nanotubeschemistry peptideschemistry proteinschemistry viral by blackbart on 2007-04-20 21:18:17 as **
  • Peptide sequence and amyloid formation; molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs.
    Structure, Vol. 12, No. 3. (2004), pp. 439-55.
    by D Zanuy, Y Porat, E Gazit, R Nussinov
    posted to alanine amyloidchemistrygeneticsmetabolism bonding computer conformation congo humans hydrogen models molecular mutation oligopeptideschemistrygeneticsmetabolism protein red simulation 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 **
  • The ARTS web server for aligning RNA tertiary structures.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (2006), pp. W412-5.
    by O Dror, R Nussinov, HJ Wolfson
    posted to acid alignmentmethods conformation interface internet nucleic rnachemistry sequence software user-computer by blackbart on 2007-04-20 21:18:17 as **
  • Triggering loops and enzyme function: identification of loops that trigger and modulate movements.
    J Mol Biol, Vol. 332, No. 1. (2003), pp. 143-59.
    by K Gunasekaran, B Ma, R Nussinov
    posted to apoenzymeschemistrymetabolism binding conformation holoenzymeschemistrymetabolism hydratasechemistrymetabolism lipasechemistrymetabolism models molecular n-acetyllactosamine phosphopyruvate protein sites synthasechemistrygeneticsmetabolism tryptophanchemistrymetabolism by blackbart on 2007-04-20 21:18:17 as **
  • Different roles of electrostatics in heat and in cold: adaptation by citrate synthase.
    Chembiochem, Vol. 5, No. 3. (2004), pp. 280-90.
    by S Kumar, R Nussinov
    posted to acid adaptation amino animals bacteria binding chickens citrate cold conformation dimerization electrostatics enzyme evolution heat molecular physiologicalgenetics protein sequence si-synthasechemistrygenetics sites stability temperature by blackbart on 2007-04-20 21:18:17 as **
  • Is allostery an intrinsic property of all dynamic proteins?
    Proteins, Vol. 57, No. 3. (2004), pp. 433-43.
    by K Gunasekaran, B Ma, R Nussinov
    posted to allosteric conformation design drug protein proteinschemistrymetabolism regulation site by blackbart on 2007-04-20 21:18:17 as **
  • How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.
    Biophys J, Vol. 88, No. 3. (2005), pp. 1552-9.
    by T Haliloglu, O Keskin, B Ma, R Nussinov
    posted to acidsanalysischemistry amino binding chemical computer conformation energy folding models molecular motion protein proteinsanalysischemistry relationship simulation sites structure-activity transfer vibration 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 **
  • Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.
    J Mol Biol, Vol. 345, No. 5. (2005), pp. 1281-94.
    by O Keskin, B Ma, R Nussinov
    posted to binding bonding conformation conserved electrostatics folding homology hydrogen models molecular protein proteinschemistrymetabolism sequence sites structural by blackbart on 2007-04-20 21:18:17 as **
  • Protein-protein docking with multiple residue conformations and residue substitutions.
    Protein Sci, Vol. 11, No. 6. (2002), pp. 1393-408.
    by DM Lorber, MK Udo, BK Shoichet
    posted to acid amino animals binding computer conformation humans ligands models molecular protein protei