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Journal Abstract Search

228 related items for PubMed ID: 25189630

  • 1. Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.
    Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM.
    J Phys Chem B; 2015 Jan 22; 119(3):976-88. PubMed ID: 25189630
    [Abstract] [Full Text] [Related]

  • 2. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
    Deng N, Flynn WF, Xia J, Vijayan RS, Zhang B, He P, Mentes A, Gallicchio E, Levy RM.
    J Comput Aided Mol Des; 2016 Sep 22; 30(9):743-751. PubMed ID: 27562018
    [Abstract] [Full Text] [Related]

  • 3. Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials.
    Xia J, Flynn W, Levy RM.
    J Chem Inf Model; 2018 Jul 23; 58(7):1356-1371. PubMed ID: 29927237
    [Abstract] [Full Text] [Related]

  • 4. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis.
    Karnati KR, Wang Y.
    J Mol Graph Model; 2019 Nov 23; 92():112-122. PubMed ID: 31351319
    [Abstract] [Full Text] [Related]

  • 5. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.
    Perryman AL, Santiago DN, Forli S, Martins DS, Olson AJ.
    J Comput Aided Mol Des; 2014 Apr 23; 28(4):429-441. PubMed ID: 24493410
    [Abstract] [Full Text] [Related]

  • 6. 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]

  • 7. Characterization of small molecule binding. I. Accurate identification of strong inhibitors in virtual screening.
    Ding B, Wang J, Li N, Wang W.
    J Chem Inf Model; 2013 Jan 28; 53(1):114-22. PubMed ID: 23259763
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  • 11. Using free energy of binding calculations to improve the accuracy of virtual screening predictions.
    Malmstrom RD, Watowich SJ.
    J Chem Inf Model; 2011 Jul 25; 51(7):1648-55. PubMed ID: 21696204
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  • 12. 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
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  • 13. The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease.
    Todd MJ, Freire E.
    Proteins; 1999 Aug 01; 36(2):147-56. PubMed ID: 10398363
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  • 14. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.
    Perola E, Walters WP, Charifson PS.
    Proteins; 2004 Aug 01; 56(2):235-49. PubMed ID: 15211508
    [Abstract] [Full Text] [Related]

  • 15. Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.
    Tiefenbrunn T, Forli S, Happer M, Gonzalez A, Tsai Y, Soltis M, Elder JH, Olson AJ, Stout CD.
    Chem Biol Drug Des; 2014 Feb 01; 83(2):141-8. PubMed ID: 23998903
    [Abstract] [Full Text] [Related]

  • 16. ReFlexIn: a flexible receptor protein-ligand docking scheme evaluated on HIV-1 protease.
    Leis S, Zacharias M.
    PLoS One; 2012 Feb 01; 7(10):e48008. PubMed ID: 23110159
    [Abstract] [Full Text] [Related]

  • 17. Using AutoDock for ligand-receptor docking.
    Morris GM, Huey R, Olson AJ.
    Curr Protoc Bioinformatics; 2008 Dec 01; Chapter 8():Unit 8.14. PubMed ID: 19085980
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  • 18. Efficient molecular docking of NMR structures: application to HIV-1 protease.
    Huang SY, Zou X.
    Protein Sci; 2007 Jan 01; 16(1):43-51. PubMed ID: 17123961
    [Abstract] [Full Text] [Related]

  • 19. Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes.
    Lu Y, Yang CY, Wang S.
    J Am Chem Soc; 2006 Sep 13; 128(36):11830-9. PubMed ID: 16953623
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  • 20. Rescoring of docking poses under Occam's Razor: are there simpler solutions?
    Zhenin M, Bahia MS, Marcou G, Varnek A, Senderowitz H, Horvath D.
    J Comput Aided Mol Des; 2018 Sep 13; 32(9):877-888. PubMed ID: 30173397
    [Abstract] [Full Text] [Related]

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