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Journal Abstract Search

779 related items for PubMed ID: 21541964

  • 1. SwissParam: a fast force field generation tool for small organic molecules.
    Zoete V, Cuendet MA, Grosdidier A, Michielin O.
    J Comput Chem; 2011 Aug; 32(11):2359-68. PubMed ID: 21541964
    [Abstract] [Full Text] [Related]

  • 2. SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization.
    Bugnon M, Goullieux M, Röhrig UF, Perez MAS, Daina A, Michielin O, Zoete V.
    J Chem Inf Model; 2023 Nov 13; 63(21):6469-6475. PubMed ID: 37853543
    [Abstract] [Full Text] [Related]

  • 3. 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 Nov 13; 23(5):457-61. PubMed ID: 20101644
    [Abstract] [Full Text] [Related]

  • 4. EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.
    Grosdidier A, Zoete V, Michielin O.
    Proteins; 2007 Jun 01; 67(4):1010-25. PubMed ID: 17380512
    [Abstract] [Full Text] [Related]

  • 5. Fast docking using the CHARMM force field with EADock DSS.
    Grosdidier A, Zoete V, Michielin O.
    J Comput Chem; 2011 Jul 30; 32(10):2149-59. PubMed ID: 21541955
    [Abstract] [Full Text] [Related]

  • 6. Combination of the CHARMM27 force field with united-atom lipid force fields.
    Sapay N, Tieleman DP.
    J Comput Chem; 2011 May 30; 32(7):1400-10. PubMed ID: 21425293
    [Abstract] [Full Text] [Related]

  • 7. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
    Schüttelkopf AW, van Aalten DM.
    Acta Crystallogr D Biol Crystallogr; 2004 Aug 30; 60(Pt 8):1355-63. PubMed ID: 15272157
    [Abstract] [Full Text] [Related]

  • 8. In silico fragment-based drug discovery: setup and validation of a fragment-to-lead computational protocol using S4MPLE.
    Hoffer L, Renaud JP, Horvath D.
    J Chem Inf Model; 2013 Apr 22; 53(4):836-51. PubMed ID: 23537132
    [Abstract] [Full Text] [Related]

  • 9. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation.
    Pei J, Wang Q, Zhou J, Lai L.
    Proteins; 2004 Dec 01; 57(4):651-64. PubMed ID: 15390269
    [Abstract] [Full Text] [Related]

  • 10. The consequences of scoring docked ligand conformations using free energy correlations.
    Spyrakis F, Amadasi A, Fornabaio M, Abraham DJ, Mozzarelli A, Kellogg GE, Cozzini P.
    Eur J Med Chem; 2007 Jul 01; 42(7):921-33. PubMed ID: 17346861
    [Abstract] [Full Text] [Related]

  • 11. 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 01; 48(12):2371-85. PubMed ID: 19007114
    [Abstract] [Full Text] [Related]

  • 12. A comprehensive docking study on the selectivity of binding of aromatic compounds to proteins.
    Hetényi C, Maran U, Karelson M.
    J Chem Inf Comput Sci; 2003 Dec 01; 43(5):1576-83. PubMed ID: 14502492
    [Abstract] [Full Text] [Related]

  • 13. Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.
    Wu G, Robertson DH, Brooks CL, Vieth M.
    J Comput Chem; 2003 Oct 01; 24(13):1549-62. PubMed ID: 12925999
    [Abstract] [Full Text] [Related]

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  • 16. CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.
    Patel S, Brooks CL.
    J Comput Chem; 2004 Jan 15; 25(1):1-15. PubMed ID: 14634989
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  • 18. [Computer drug design based on analysis of a target macromolecule structure. I. Search and description of a ligand binding site in a target molecule].
    Ivanov AS, Dubanov AV, Skvortsov VS, Archakov AI.
    Vopr Med Khim; 2002 Jan 15; 48(3):304-15. PubMed ID: 12243090
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  • 20. RosettaLigand docking with full ligand and receptor flexibility.
    Davis IW, Baker D.
    J Mol Biol; 2009 Jan 16; 385(2):381-92. PubMed ID: 19041878
    [Abstract] [Full Text] [Related]

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