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Journal Abstract Search


210 related items for PubMed ID: 9034363

  • 1. Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm.
    Raymer ML, Sanschagrin PC, Punch WF, Venkataraman S, Goodman ED, Kuhn LA.
    J Mol Biol; 1997 Jan 31; 265(4):445-64. PubMed ID: 9034363
    [Abstract] [Full Text] [Related]

  • 2. Classification of water molecules in protein binding sites.
    Barillari C, Taylor J, Viner R, Essex JW.
    J Am Chem Soc; 2007 Mar 07; 129(9):2577-87. PubMed ID: 17288418
    [Abstract] [Full Text] [Related]

  • 3. Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes.
    Lu Y, Wang R, Yang CY, Wang S.
    J Chem Inf Model; 2007 Mar 07; 47(2):668-75. PubMed ID: 17266298
    [Abstract] [Full Text] [Related]

  • 4. Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules.
    Amadasi A, Spyrakis F, Cozzini P, Abraham DJ, Kellogg GE, Mozzarelli A.
    J Mol Biol; 2006 Apr 21; 358(1):289-309. PubMed ID: 16497327
    [Abstract] [Full Text] [Related]

  • 5. Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy.
    Gauto DF, Di Lella S, Guardia CM, Estrin DA, Martí MA.
    J Phys Chem B; 2009 Jun 25; 113(25):8717-24. PubMed ID: 19485380
    [Abstract] [Full Text] [Related]

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  • 7. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity.
    Sanschagrin PC, Kuhn LA.
    Protein Sci; 1998 Oct 25; 7(10):2054-64. PubMed ID: 9792092
    [Abstract] [Full Text] [Related]

  • 8. Domain-based small molecule binding site annotation.
    Snyder KA, Feldman HJ, Dumontier M, Salama JJ, Hogue CW.
    BMC Bioinformatics; 2006 Mar 17; 7():152. PubMed ID: 16545112
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  • 10. Statistical and molecular dynamics studies of buried waters in globular proteins.
    Park S, Saven JG.
    Proteins; 2005 Aug 15; 60(3):450-63. PubMed ID: 15937899
    [Abstract] [Full Text] [Related]

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  • 12. Nonequilibrium, multiple-timescale simulations of ligand-receptor interactions in structured protein systems.
    Zhang Y, Peters MH, Li Y.
    Proteins; 2003 Aug 15; 52(3):339-48. PubMed ID: 12866048
    [Abstract] [Full Text] [Related]

  • 13. Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica.
    Koellner G, Kryger G, Millard CB, Silman I, Sussman JL, Steiner T.
    J Mol Biol; 2000 Feb 18; 296(2):713-35. PubMed ID: 10669619
    [Abstract] [Full Text] [Related]

  • 14. Crystal structure of a glutamate/aspartate binding protein complexed with a glutamate molecule: structural basis of ligand specificity at atomic resolution.
    Hu Y, Fan CP, Fu G, Zhu D, Jin Q, Wang DC.
    J Mol Biol; 2008 Sep 26; 382(1):99-111. PubMed ID: 18640128
    [Abstract] [Full Text] [Related]

  • 15. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
    Najmanovich R, Kurbatova N, Thornton J.
    Bioinformatics; 2008 Aug 15; 24(16):i105-11. PubMed ID: 18689810
    [Abstract] [Full Text] [Related]

  • 16. Ligand-protein docking with water molecules.
    Roberts BC, Mancera RL.
    J Chem Inf Model; 2008 Feb 15; 48(2):397-408. PubMed ID: 18211049
    [Abstract] [Full Text] [Related]

  • 17. The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.
    Peters KP, Fauck J, Frömmel C.
    J Mol Biol; 1996 Feb 16; 256(1):201-13. PubMed ID: 8609611
    [Abstract] [Full Text] [Related]

  • 18. ProMate: a structure based prediction program to identify the location of protein-protein binding sites.
    Neuvirth H, Raz R, Schreiber G.
    J Mol Biol; 2004 Apr 16; 338(1):181-99. PubMed ID: 15050833
    [Abstract] [Full Text] [Related]

  • 19. HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.
    Floriano WB, Vaidehi N, Zamanakos G, Goddard WA.
    J Med Chem; 2004 Jan 01; 47(1):56-71. PubMed ID: 14695820
    [Abstract] [Full Text] [Related]

  • 20. N-H...O, O-H...O, and C-H...O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition.
    Sarkhel S, Desiraju GR.
    Proteins; 2004 Feb 01; 54(2):247-59. PubMed ID: 14696187
    [Abstract] [Full Text] [Related]


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