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Journal Abstract Search

191 related items for PubMed ID: 20839830

  • 1. 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]

  • 2. 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 07; 25(3):223-35. PubMed ID: 21286784
    [Abstract] [Full Text] [Related]

  • 3. Ligand conformational and solvation/desolvation free energy in protein-ligand complex formation.
    Kolár M, Fanfrlík J, Hobza P.
    J Phys Chem B; 2011 Apr 28; 115(16):4718-24. PubMed ID: 21466174
    [Abstract] [Full Text] [Related]

  • 4. A semiempirical free energy force field with charge-based desolvation.
    Huey R, Morris GM, Olson AJ, Goodsell DS.
    J Comput Chem; 2007 Apr 30; 28(6):1145-52. PubMed ID: 17274016
    [Abstract] [Full Text] [Related]

  • 5. Semiempirical quantum mechanical method PM6-DH2X describes the geometry and energetics of CK2-inhibitor complexes involving halogen bonds well, while the empirical potential fails.
    Dobes P, Rezác J, Fanfrlík J, Otyepka M, Hobza P.
    J Phys Chem B; 2011 Jul 07; 115(26):8581-9. PubMed ID: 21648479
    [Abstract] [Full Text] [Related]

  • 6. AMBER empirical potential describes the geometry and energy of noncovalent halogen interactions better than advanced semiempirical quantum mechanical method PM6-DH2X.
    Ibrahim MA.
    J Phys Chem B; 2012 Mar 22; 116(11):3659-69. PubMed ID: 22393912
    [Abstract] [Full Text] [Related]

  • 7. Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods.
    Nagy G, Gyurcsik B, Hoffmann EA, Körtvélyesi T.
    J Mol Graph Model; 2011 Jun 22; 29(7):928-34. PubMed ID: 21470886
    [Abstract] [Full Text] [Related]

  • 8. Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes.
    Raha K, Merz KM.
    J Med Chem; 2005 Jul 14; 48(14):4558-75. PubMed ID: 15999994
    [Abstract] [Full Text] [Related]

  • 9. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors.
    Wittayanarakul K, Hannongbua S, Feig M.
    J Comput Chem; 2008 Apr 15; 29(5):673-85. PubMed ID: 17849388
    [Abstract] [Full Text] [Related]

  • 10. An estimation method of binding free energy in terms of ABEEMσπ/MM and continuum electrostatics fused into LIE method.
    Chen SL, Zhao DX, Yang ZZ.
    J Comput Chem; 2011 Jan 30; 32(2):338-48. PubMed ID: 20662079
    [Abstract] [Full Text] [Related]

  • 11. A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect.
    Lee J, Seok C.
    Proteins; 2008 Feb 15; 70(3):1074-83. PubMed ID: 18076034
    [Abstract] [Full Text] [Related]

  • 12. Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease.
    Fong P, McNamara JP, Hillier IH, Bryce RA.
    J Chem Inf Model; 2009 Apr 15; 49(4):913-24. PubMed ID: 19309119
    [Abstract] [Full Text] [Related]

  • 13. A semiempirical approach to ligand-binding affinities: dependence on the Hamiltonian and corrections.
    Mikulskis P, Genheden S, Wichmann K, Ryde U.
    J Comput Chem; 2012 May 05; 33(12):1179-89. PubMed ID: 22396176
    [Abstract] [Full Text] [Related]

  • 14. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases.
    Stoica I, Sadiq SK, Coveney PV.
    J Am Chem Soc; 2008 Feb 27; 130(8):2639-48. PubMed ID: 18225901
    [Abstract] [Full Text] [Related]

  • 15. De novo ligand design to an ensemble of protein structures.
    Todorov NP, Buenemann CL, Alberts IL.
    Proteins; 2006 Jul 01; 64(1):43-59. PubMed ID: 16555306
    [Abstract] [Full Text] [Related]

  • 16. E-novo: an automated workflow for efficient structure-based lead optimization.
    Pearce BC, Langley DR, Kang J, Huang H, Kulkarni A.
    J Chem Inf Model; 2009 Jul 01; 49(7):1797-809. PubMed ID: 19552372
    [Abstract] [Full Text] [Related]

  • 17. 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]

  • 18. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.
    Pérez C, Pastor M, Ortiz AR, Gago F.
    J Med Chem; 1998 Mar 12; 41(6):836-52. PubMed ID: 9526559
    [Abstract] [Full Text] [Related]

  • 19. Rational automatic search method for stable docking models of protein and ligand.
    Mizutani MY, Tomioka N, Itai A.
    J Mol Biol; 1994 Oct 21; 243(2):310-26. PubMed ID: 7932757
    [Abstract] [Full Text] [Related]

  • 20. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.
    Bryce RA.
    Future Med Chem; 2011 Apr 21; 3(6):683-98. PubMed ID: 21554075
    [Abstract] [Full Text] [Related]

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