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261 related items for PubMed ID: 19399779

  • 21. Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: application to influenza neuraminidase.
    Bonnet P, Bryce RA.
    J Mol Graph Model; 2005 Oct; 24(2):147-56. PubMed ID: 16098779
    [Abstract] [Full Text] [Related]

  • 22. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.
    Gohlke H, Case DA.
    J Comput Chem; 2004 Jan 30; 25(2):238-50. PubMed ID: 14648622
    [Abstract] [Full Text] [Related]

  • 23. Thermodynamic analysis of binding of p-substituted benzamidines to trypsin.
    Talhout R, Engberts JB.
    Eur J Biochem; 2001 Mar 30; 268(6):1554-60. PubMed ID: 11248672
    [Abstract] [Full Text] [Related]

  • 24. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.
    Schnieders MJ, Baker NA, Ren P, Ponder JW.
    J Chem Phys; 2007 Mar 28; 126(12):124114. PubMed ID: 17411115
    [Abstract] [Full Text] [Related]

  • 25. Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models.
    Wagoner J, Baker NA.
    J Comput Chem; 2004 Oct 28; 25(13):1623-9. PubMed ID: 15264256
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  • 26. Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.
    Godschalk F, Genheden S, Söderhjelm P, Ryde U.
    Phys Chem Chem Phys; 2013 May 28; 15(20):7731-9. PubMed ID: 23595060
    [Abstract] [Full Text] [Related]

  • 27. Computer simulation of protein-ligand interactions: challenges and applications.
    Hassan SA, Gracia L, Vasudevan G, Steinbach PJ.
    Methods Mol Biol; 2005 May 28; 305():451-92. PubMed ID: 15940011
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  • 28. A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.
    Yamagishi J, Okimoto N, Morimoto G, Taiji M.
    J Comput Chem; 2014 Nov 05; 35(29):2132-9. PubMed ID: 25220475
    [Abstract] [Full Text] [Related]

  • 29. 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
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  • 30. 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
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  • 31. Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties.
    Brandt T, Holzmann N, Muley L, Khayat M, Wegscheid-Gerlach C, Baum B, Heine A, Hangauer D, Klebe G.
    J Mol Biol; 2011 Feb 04; 405(5):1170-87. PubMed ID: 21111747
    [Abstract] [Full Text] [Related]

  • 32. Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models.
    Cumberworth A, Bui JM, Gsponer J.
    J Comput Chem; 2016 Mar 15; 37(7):629-40. PubMed ID: 26558440
    [Abstract] [Full Text] [Related]

  • 33. A semi-implicit solvent model for the simulation of peptides and proteins.
    Basdevant N, Borgis D, Ha-Duong T.
    J Comput Chem; 2004 Jun 15; 25(8):1015-29. PubMed ID: 15067677
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  • 34. Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters.
    Geerke DP, van Gunsteren WF.
    J Phys Chem B; 2007 Jun 14; 111(23):6425-36. PubMed ID: 17508737
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  • 35. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
    Patel S, Mackerell AD, Brooks CL.
    J Comput Chem; 2004 Sep 14; 25(12):1504-14. PubMed ID: 15224394
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  • 36. Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3.
    He X, Man VH, Ji B, Xie XQ, Wang J.
    J Comput Aided Mol Des; 2019 Jan 14; 33(1):105-117. PubMed ID: 30218199
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  • 37. Computational analysis of binding of P1 variants to trypsin.
    Brandsdal BO, Aqvist J, Smalås AO.
    Protein Sci; 2001 Aug 14; 10(8):1584-95. PubMed ID: 11468355
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  • 38. Halothane solvation in water and organic solvents from molecular simulations with new polarizable potential function.
    Subbotina JO, Johannes J, Lev B, Noskov SY.
    J Phys Chem B; 2010 May 20; 114(19):6401-8. PubMed ID: 20411978
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  • 39. 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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  • 40. Thermodynamic stability of hydrogen-bonded systems in polar and nonpolar environments.
    Pasalić H, Aquino AJ, Tunega D, Haberhauer G, Gerzabek MH, Georg HC, Moraes TF, Coutinho K, Canuto S, Lischka H.
    J Comput Chem; 2010 Jul 30; 31(10):2046-55. PubMed ID: 20127744
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