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Journal Abstract Search

166 related items for PubMed ID: 15725015

  • 1. Flexible docking in solution using metadynamics.
    Gervasio FL, Laio A, Parrinello M.
    J Am Chem Soc; 2005 Mar 02; 127(8):2600-7. PubMed ID: 15725015
    [Abstract] [Full Text] [Related]

  • 2. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4.
    Morris GM, Goodsell DS, Huey R, Olson AJ.
    J Comput Aided Mol Des; 1996 Aug 02; 10(4):293-304. PubMed ID: 8877701
    [Abstract] [Full Text] [Related]

  • 3. Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.
    Jiao D, Zhang J, Duke RE, Li G, Schnieders MJ, Ren P.
    J Comput Chem; 2009 Aug 02; 30(11):1701-11. PubMed ID: 19399779
    [Abstract] [Full Text] [Related]

  • 4. Receptor rigidity and ligand mobility in trypsin-ligand complexes.
    Guvench O, Price DJ, Brooks CL.
    Proteins; 2005 Feb 01; 58(2):407-17. PubMed ID: 15578663
    [Abstract] [Full Text] [Related]

  • 5. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures.
    Barril X, Morley SD.
    J Med Chem; 2005 Jun 30; 48(13):4432-43. PubMed ID: 15974595
    [Abstract] [Full Text] [Related]

  • 6. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation.
    Mangoni M, Roccatano D, Di Nola A.
    Proteins; 1999 May 01; 35(2):153-62. PubMed ID: 10223288
    [Abstract] [Full Text] [Related]

  • 7. Exploring the Ligand Binding/Unbinding Pathway by Selectively Enhanced Sampling of Ligand in a Protein-Ligand Complex.
    Shao Q, Zhu W.
    J Phys Chem B; 2019 Sep 26; 123(38):7974-7983. PubMed ID: 31478672
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  • 9. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.
    Buch I, Giorgino T, De Fabritiis G.
    Proc Natl Acad Sci U S A; 2011 Jun 21; 108(25):10184-9. PubMed ID: 21646537
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  • 11. Computer simulation of protein-ligand interactions: challenges and applications.
    Hassan SA, Gracia L, Vasudevan G, Steinbach PJ.
    Methods Mol Biol; 2005 Jun 21; 305():451-92. PubMed ID: 15940011
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  • 13. Protein flexibility in ligand docking and virtual screening to protein kinases.
    Cavasotto CN, Abagyan RA.
    J Mol Biol; 2004 Mar 12; 337(1):209-25. PubMed ID: 15001363
    [Abstract] [Full Text] [Related]

  • 14. Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models.
    Plattner N, Noé F.
    Nat Commun; 2015 Jul 02; 6():7653. PubMed ID: 26134632
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  • 16. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.
    Votapka LW, Jagger BR, Heyneman AL, Amaro RE.
    J Phys Chem B; 2017 Apr 20; 121(15):3597-3606. PubMed ID: 28191969
    [Abstract] [Full Text] [Related]

  • 17. Electrostatic effects play a central role in cold adaptation of trypsin.
    Brandsdal BO, Smalås AO, Aqvist J.
    FEBS Lett; 2001 Jun 15; 499(1-2):171-5. PubMed ID: 11418134
    [Abstract] [Full Text] [Related]

  • 18. Gaussian docking functions.
    McGann MR, Almond HR, Nicholls A, Grant JA, Brown FK.
    Biopolymers; 2003 Jan 15; 68(1):76-90. PubMed ID: 12579581
    [Abstract] [Full Text] [Related]

  • 19. Trypsin-ligand binding free energy calculation with AMOEBA.
    Shi Y, Jiao D, Schnieders MJ, Ren P.
    Annu Int Conf IEEE Eng Med Biol Soc; 2009 Jan 15; 2009():2328-31. PubMed ID: 19965178
    [Abstract] [Full Text] [Related]

  • 20. Comparative molecular modeling analysis of-5-amidinoindole and benzamidine binding to thrombin and trypsin: specific H-bond formation contributes to high 5-amidinoindole potency and selectivity for thrombin and factor Xa.
    Zhou Y, Johnson ME.
    J Mol Recognit; 1999 Jan 15; 12(4):235-41. PubMed ID: 10440994
    [Abstract] [Full Text] [Related]

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