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Journal Abstract Search

224 related items for PubMed ID: 9141130

  • 21. FURSMASA: a new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data.
    Pearlman DA, Rao BG, Charifson P.
    Proteins; 2008 May 15; 71(3):1519-38. PubMed ID: 18300249
    [Abstract] [Full Text] [Related]

  • 22. 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]

  • 23. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
    Wang W, Wang J, Kollman PA.
    Proteins; 1999 Feb 15; 34(3):395-402. PubMed ID: 10024025
    [Abstract] [Full Text] [Related]

  • 24. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.
    Liu Z, Dominy BN, Shakhnovich EI.
    J Am Chem Soc; 2004 Jul 14; 126(27):8515-28. PubMed ID: 15238009
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  • 25. Assessment of solvation effects on calculated binding affinity differences: trypsin inhibition by flavonoids as a model system for congeneric series.
    Checa A, Ortiz AR, de Pascual-Teresa B, Gago F.
    J Med Chem; 1997 Dec 05; 40(25):4136-45. PubMed ID: 9406602
    [Abstract] [Full Text] [Related]

  • 26. A pharmacophore docking algorithm and its application to the cross-docking of 18 HIV-NNRTI's in their binding pockets.
    Daeyaert F, de Jonge M, Heeres J, Koymans L, Lewi P, Vinkers MH, Janssen PA.
    Proteins; 2004 Feb 15; 54(3):526-33. PubMed ID: 14748000
    [Abstract] [Full Text] [Related]

  • 27. PEARLS: program for energetic analysis of receptor-ligand system.
    Han LY, Lin HH, Li ZR, Zheng CJ, Cao ZW, Xie B, Chen YZ.
    J Chem Inf Model; 2006 Feb 15; 46(1):445-50. PubMed ID: 16426079
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  • 28. A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI.
    Gong XQ, Chang S, Zhang QH, Li CH, Shen LZ, Ma XH, Wang MH, Liu B, He HQ, Chen WZ, Wang CX.
    Proteins; 2007 Dec 01; 69(4):859-65. PubMed ID: 17803223
    [Abstract] [Full Text] [Related]

  • 29. An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes.
    Jain T, Jayaram B.
    FEBS Lett; 2005 Dec 05; 579(29):6659-66. PubMed ID: 16307743
    [Abstract] [Full Text] [Related]

  • 30. SuperStar: improved knowledge-based interaction fields for protein binding sites.
    Verdonk ML, Cole JC, Watson P, Gillet V, Willett P.
    J Mol Biol; 2001 Mar 30; 307(3):841-59. PubMed ID: 11273705
    [Abstract] [Full Text] [Related]

  • 31. Flexible ligand docking: a multistep strategy approach.
    Wang J, Kollman PA, Kuntz ID.
    Proteins; 1999 Jul 01; 36(1):1-19. PubMed ID: 10373002
    [Abstract] [Full Text] [Related]

  • 32. 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
    [Abstract] [Full Text] [Related]

  • 33. Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition.
    Ma XH, Li CH, Shen LZ, Gong XQ, Chen WZ, Wang CX.
    Proteins; 2005 Aug 01; 60(2):319-23. PubMed ID: 15981260
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  • 34. Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.
    Zoete V, Grosdidier A, Cuendet M, Michielin O.
    J Mol Recognit; 2010 Aug 01; 23(5):457-61. PubMed ID: 20101644
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  • 35. Ligand-protein docking using a quantum stochastic tunneling optimization method.
    Mancera RL, Källblad P, Todorov NP.
    J Comput Chem; 2004 Apr 30; 25(6):858-64. PubMed ID: 15011257
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  • 36. Electrostatics in proteins and protein-ligand complexes.
    Kukić P, Nielsen JE.
    Future Med Chem; 2010 Apr 30; 2(4):647-66. PubMed ID: 21426012
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  • 37. Protein-ligand docking using mutually orthogonal Latin squares (MOLSDOCK).
    Viji SN, Prasad PA, Gautham N.
    J Chem Inf Model; 2009 Dec 30; 49(12):2687-94. PubMed ID: 19968302
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  • 38. Computing van der Waals energies in the context of the rotamer approximation.
    Grigoryan G, Ochoa A, Keating AE.
    Proteins; 2007 Sep 01; 68(4):863-78. PubMed ID: 17554777
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  • 39. Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.
    van Lipzig MM, ter Laak AM, Jongejan A, Vermeulen NP, Wamelink M, Geerke D, Meerman JH.
    J Med Chem; 2004 Feb 12; 47(4):1018-30. PubMed ID: 14761204
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  • 40. Lead finder: an approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening.
    Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, Chilov GG.
    J Chem Inf Model; 2008 Dec 12; 48(12):2371-85. PubMed ID: 19007114
    [Abstract] [Full Text] [Related]

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