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blackbart binding [113 articles]

Recent papers added to blackbart library classified by the tag binding. You can also see everyone's binding.
  • 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 **
  • 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 **
  • Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces.
    Proc Natl Acad Sci U S A, Vol. 100, No. 10. (2003), pp. 5772-7.
    by B Ma, T Elkayam, H Wolfson, R Nussinov
    posted to acid alignment amino binding conserved data epitopeschemistry homology molecular proteinschemistry sequence sites tryptophan 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 **
  • 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 **
  • 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 **
  • Association of putative concave protein-binding sites with the fluctuation behavior of residues.
    Protein Sci, Vol. 15, No. 10. (2006), pp. 2265-77.
    by A Ertekin, R Nussinov, T Haliloglu
    posted to acidschemistry amino binding models molecular motion proteinschemistrymetabolism sites software vibration 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.
    J Mol Biol, Vol. 344, No. 3. (2004), pp. 781-95.
    by X Li, O Keskin, B Ma, R Nussinov, J Liang
    posted to binding models molecular protein proteinschemistrymetabolism thermodynamics 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 **
  • 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 **
  • Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions.
    Proteins, Vol. 61, No. 1. (2005), pp. 6-20.
    by S Mintz, Shulman A Peleg, HJ Wolfson, R Nussinov
    posted to binding chemistry crystallography databases folding homology internet models molecular physical protein proteinschemistrymetabolism quaternary structural structure x-ray 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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-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 proteinschemistrygeneticsmetabolism simulation substitution bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Structure-based design of inhibitors specific for bacterial thymidylate synthase.
    Biochemistry, Vol. 38, No. 5. (1999), pp. 1607-17.
    by TJ Stout, D Tondi, M Rinaldi, D Barlocco, P Pecorari, DV Santi, ID Kuntz, RM Stroud, BK Shoichet, MP Costi
    posted to acid amino bacterial binding caseienzymology computer crystallography enzyme humans inhibitorschemical inhibitorsgenetics lactobacillus models molecular mutagenesis phenolphthaleinchemical proteinsantagonists simulation site-directed sites species specificity substitutiongenetics substrate synthaseantagonists synthesispharmacology thymidylate x-ray bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Structural aspects for evolution of beta-lactamases from penicillin-binding proteins.
    J Am Chem Soc, Vol. 125, No. 32. (2003), pp. 9612-8.
    by SO Meroueh, G Minasov, W Lee, BK Shoichet, S Mobashery
    posted to bacterial beta-lactamaseschemistrygeneticsmetabolism binding carboxypeptidasechemistrygeneticsmetabolism carrier cephalosporinschemical colienzymology computer conformation crystallography escherichia evolution hexosyltransferaseschemistrygeneticsmetabolism models molecular muramoylpentapeptide penicillin-binding peptidoglycanchemistrymetabolism peptidyl protein proteins proteinschemistrygeneticsmetabolism simulation sites synthesischemistrymetabolism transferaseschemistrygeneticsmetabolism x-ray bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Probing molecular docking in a charged model binding site.
    J Mol Biol, Vol. 357, No. 5. (2006), pp. 1449-70.
    by R Brenk, SW Vetter, SE Boyce, DB Goodin, BK Shoichet
    posted to amidineschemistry amineschemistry binding conformation crystallography cytochrome-c data esterschemistry ligands models molecular peroxidasechemistrygeneticsmetabolism protein sequence sites structure x-ray bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Prediction of protein-ligand interactions. Docking and scoring: successes and gaps.
    J Med Chem, Vol. 49, No. 20. (2006), pp. 5851-5.
    by AR Leach, BK Shoichet, CE Peishoff
    posted to binding design drug ligands models molecular protein proteinschemistry quantitative relationship sites structure-activity bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site.
    Biochemistry, Vol. 40, No. 27. (2001), pp. 7992-9.
    by I Trehan, BM Beadle, BK Shoichet
    posted to acid alaninegenetics amino asparaginegenetics bacterial beta-lactamasesantagonists binding colienzymologygenetics crystallization crystallography denaturation effectsgenetics enzyme escherichia imipenempharmacology inhibitorsgeneticsmetabolism kinetics moxalactampharmacology mutagenesis protein proteins site-directed sitesdrug stabilitydrug substitutiongenetics thermodynamics x-ray bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Ligand solvation in molecular docking.
    Proteins, Vol. 34, No. 1. (1999), pp. 4-16.
    by BK Shoichet, AR Leach, ID Kuntz
    posted to aniline binding compoundschemistry computer databases dehydrogenasechemistry factual indoleschemistry kinetics ligands lysosomeschemistry models molecular monophosphatechemistry protein pteridineschemistry simulation sites tetrahydrofolate thymidine 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 **
  • Lead discovery using molecular docking.
    Curr Opin Chem Biol, Vol. 6, No. 4. (2002), pp. 439-46.
    by BK Shoichet, SL Mcgovern, B Wei, JJ Irwin
    posted to animals binding computer delivery design drug humans models molecular protein simulation systems bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Using steric hindrance to design new inhibitors of class C beta-lactamases.
    Chem Biol, Vol. 9, No. 9. (2002), pp. 971-80.
    by I Trehan, F Morandi, LC Blaszczak, BK Shoichet
    posted to acylation agentschemistrymetabolismpharmacology anti-bacterial beta-lactam beta-lactamasesantagonists beta-lactams binding conformation crystallography design drug enzyme humans hydrolysis inhibitorschemistrymetabolismpharmacology inhibitorsclassificationmetabolism kinetics microbial models molecular relationship resistance sensitivity sites structure-activity tests x-ray bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Structure-based enhancement of boronic acid-based inhibitors of AmpC beta-lactamase.
    J Med Chem, Vol. 41, No. 23. (1998), pp. 4577-86.
    by GS Weston, J Blazquez, F Baquero, BK Shoichet
    posted to acidschemistry agentschemical anti-bacterial bacterial beta-lactam beta-lactamasesantagonists binding boronic cloacaedrug colidrug crystallography drug effects effectsenzymology enterobacter enzyme escherichia inhibitorschemical inhibitorsmetabolism microbial models molecular proteins relationship resistance sensitivity sites structure-activity synergism synthesischemistrymetabolismpharmacology tests thiophenes x-ray bibtex-import by blackbart on 2007-04-20 21:16:38 as **
  • Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation.
    Protein Sci, Vol. 10, No. 6. (2001), pp. 1254-9.
    by BM Beadle, RA Nicholas, BK Shoichet
    posted to acylation agentsmetabolism anti-bacterial bacterial beta-lactamsmetabolism binding carboxypeptidasemetabolism carrier cefoxitinmetabolism chemical circular cloxacillinmetabolism colimetabolism denaturation dichroism escherichia fluorescence hexosyltransferases imipenemmetabolism models moxalactammetabolism muramoylpentapeptide penicillin-binding peptidyl protein proteins proteinsmetabolism spectrometry temperature thermodynamics transferases 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 **
  • Soft docking and multiple receptor conformations in virtual screening.
    J Med Chem, Vol. 47, No. 21. (2004), pp. 5076-84.
    by AM Ferrari, BQ Wei, L Costantino, BK Shoichet
    posted to aldehyde bacteriophage binding conformation ligands models