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Journal Abstract Search

188 related items for PubMed ID: 22476578

  • 1. Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores.
    Benson ML, Faver JC, Ucisik MN, Dashti DS, Zheng Z, Merz KM.
    J Comput Aided Mol Des; 2012 May; 26(5):647-59. PubMed ID: 22476578
    [Abstract] [Full Text] [Related]

  • 2. PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.
    Tang YT, Marshall GR.
    J Chem Inf Model; 2011 Feb 28; 51(2):214-28. PubMed ID: 21214225
    [Abstract] [Full Text] [Related]

  • 3. Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.
    Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson MK.
    J Comput Aided Mol Des; 2012 May 28; 26(5):475-87. PubMed ID: 22366955
    [Abstract] [Full Text] [Related]

  • 4. A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands.
    Fanfrlík J, Bronowska AK, Rezác J, Prenosil O, Konvalinka J, Hobza P.
    J Phys Chem B; 2010 Oct 07; 114(39):12666-78. PubMed ID: 20839830
    [Abstract] [Full Text] [Related]

  • 5. Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation.
    Grudinin S, Kadukova M, Eisenbarth A, Marillet S, Cazals F.
    J Comput Aided Mol Des; 2016 Sep 07; 30(9):791-804. PubMed ID: 27718029
    [Abstract] [Full Text] [Related]

  • 6. Structural parameterization of the binding enthalpy of small ligands.
    Luque I, Freire E.
    Proteins; 2002 Nov 01; 49(2):181-90. PubMed ID: 12210999
    [Abstract] [Full Text] [Related]

  • 7. A fragment-based approach to the SAMPL3 Challenge.
    Kulp JL, Blumenthal SN, Wang Q, Bryan RL, Guarnieri F.
    J Comput Aided Mol Des; 2012 May 01; 26(5):583-94. PubMed ID: 22290624
    [Abstract] [Full Text] [Related]

  • 8. Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations.
    Ben-Shalom IY, Pfeiffer-Marek S, Baringhaus KH, Gohlke H.
    J Chem Inf Model; 2017 Feb 27; 57(2):170-189. PubMed ID: 27996253
    [Abstract] [Full Text] [Related]

  • 9. Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.
    Dobeš P, Fanfrlík J, Rezáč J, Otyepka M, Hobza P.
    J Comput Aided Mol Des; 2011 Mar 27; 25(3):223-35. PubMed ID: 21286784
    [Abstract] [Full Text] [Related]

  • 10. Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions.
    Huang SY, Zou X.
    J Chem Inf Model; 2010 Feb 22; 50(2):262-73. PubMed ID: 20088605
    [Abstract] [Full Text] [Related]

  • 11. Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK.
    Kasper P, Christen P, Gehring H.
    Proteins; 2000 Aug 01; 40(2):185-92. PubMed ID: 10842335
    [Abstract] [Full Text] [Related]

  • 12. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.
    Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U.
    J Am Chem Soc; 2011 Aug 24; 133(33):13081-92. PubMed ID: 21728337
    [Abstract] [Full Text] [Related]

  • 13. Develop and test a solvent accessible surface area-based model in conformational entropy calculations.
    Wang J, Hou T.
    J Chem Inf Model; 2012 May 25; 52(5):1199-212. PubMed ID: 22497310
    [Abstract] [Full Text] [Related]

  • 14. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.
    Misini Ignjatović M, Caldararu O, Dong G, Muñoz-Gutierrez C, Adasme-Carreño F, Ryde U.
    J Comput Aided Mol Des; 2016 Sep 25; 30(9):707-730. PubMed ID: 27565797
    [Abstract] [Full Text] [Related]

  • 15. Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method.
    Mazanetz MP, Ichihara O, Law RJ, Whittaker M.
    J Cheminform; 2011 Jan 10; 3(1):2. PubMed ID: 21219630
    [Abstract] [Full Text] [Related]

  • 16. Influence of the solvent representation on vibrational entropy calculations: generalized born versus distance-dependent dielectric model.
    Kopitz H, Cashman DA, Pfeiffer-Marek S, Gohlke H.
    J Comput Chem; 2012 Apr 05; 33(9):1004-13. PubMed ID: 22298332
    [Abstract] [Full Text] [Related]

  • 17. Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities.
    Gao C, Park MS, Stern HA.
    Biophys J; 2010 Mar 03; 98(5):901-10. PubMed ID: 20197044
    [Abstract] [Full Text] [Related]

  • 18. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
    Sham YY, Chu ZT, Tao H, Warshel A.
    Proteins; 2000 Jun 01; 39(4):393-407. PubMed ID: 10813821
    [Abstract] [Full Text] [Related]

  • 19. Virtual screening using molecular simulations.
    Yang T, Wu JC, Yan C, Wang Y, Luo R, Gonzales MB, Dalby KN, Ren P.
    Proteins; 2011 Jun 01; 79(6):1940-51. PubMed ID: 21491494
    [Abstract] [Full Text] [Related]

  • 20. Calculations of solute and solvent entropies from molecular dynamics simulations.
    Carlsson J, Aqvist J.
    Phys Chem Chem Phys; 2006 Dec 14; 8(46):5385-95. PubMed ID: 17119645
    [Abstract] [Full Text] [Related]

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