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Journal Abstract Search

156 related items for PubMed ID: 29054096

  • 1. Simplified AutoDock force field for hydrated binding sites.
    Wojciechowski M.
    J Mol Graph Model; 2017 Nov; 78():74-80. PubMed ID: 29054096
    [Abstract] [Full Text] [Related]

  • 2. Hydration properties of ligands and drugs in protein binding sites: tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies.
    García-Sosa AT.
    J Chem Inf Model; 2013 Jun 24; 53(6):1388-405. PubMed ID: 23662606
    [Abstract] [Full Text] [Related]

  • 3. Using AutoDock for ligand-receptor docking.
    Morris GM, Huey R, Olson AJ.
    Curr Protoc Bioinformatics; 2008 Dec 24; Chapter 8():Unit 8.14. PubMed ID: 19085980
    [Abstract] [Full Text] [Related]

  • 4. Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks.
    Rudling A, Orro A, Carlsson J.
    J Chem Inf Model; 2018 Feb 26; 58(2):350-361. PubMed ID: 29308882
    [Abstract] [Full Text] [Related]

  • 5. Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.
    Hogues H, Sulea T, Gaudreault F, Corbeil CR, Purisima EO.
    J Comput Aided Mol Des; 2018 Jan 26; 32(1):143-150. PubMed ID: 28983727
    [Abstract] [Full Text] [Related]

  • 6. Development and validation of a modular, extensible docking program: DOCK 5.
    Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC.
    J Comput Aided Mol Des; 2006 Jan 26; 20(10-11):601-19. PubMed ID: 17149653
    [Abstract] [Full Text] [Related]

  • 7. 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 26; 30(9):791-804. PubMed ID: 27718029
    [Abstract] [Full Text] [Related]

  • 8. Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model.
    Kumar A, Zhang KYJ.
    J Comput Aided Mol Des; 2019 Dec 26; 33(12):1045-1055. PubMed ID: 31463704
    [Abstract] [Full Text] [Related]

  • 9. Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization.
    Liu J, He X, Zhang JZ.
    J Chem Inf Model; 2013 Jun 24; 53(6):1306-14. PubMed ID: 23651068
    [Abstract] [Full Text] [Related]

  • 10. Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.
    Greenidge PA, Kramer C, Mozziconacci JC, Sherman W.
    J Chem Inf Model; 2014 Oct 27; 54(10):2697-717. PubMed ID: 25266271
    [Abstract] [Full Text] [Related]

  • 11. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.
    Wang Z, Sun H, Yao X, Li D, Xu L, Li Y, Tian S, Hou T.
    Phys Chem Chem Phys; 2016 May 14; 18(18):12964-75. PubMed ID: 27108770
    [Abstract] [Full Text] [Related]

  • 12. AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.
    Uehara S, Tanaka S.
    Molecules; 2016 Nov 23; 21(11):. PubMed ID: 27886114
    [Abstract] [Full Text] [Related]

  • 13. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.
    Forli S, Olson AJ.
    J Med Chem; 2012 Jan 26; 55(2):623-38. PubMed ID: 22148468
    [Abstract] [Full Text] [Related]

  • 14. Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.
    Brylinski M.
    J Chem Inf Model; 2013 Nov 25; 53(11):3097-112. PubMed ID: 24171431
    [Abstract] [Full Text] [Related]

  • 15. A general and fast scoring function for protein-ligand interactions: a simplified potential approach.
    Muegge I, Martin YC.
    J Med Chem; 1999 Mar 11; 42(5):791-804. PubMed ID: 10072678
    [Abstract] [Full Text] [Related]

  • 16. Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP.
    Bayden AS, Moustakas DT, Joseph-McCarthy D, Lamb ML.
    J Chem Inf Model; 2015 Aug 24; 55(8):1552-65. PubMed ID: 26176600
    [Abstract] [Full Text] [Related]

  • 17. Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions.
    Xu X, Qiu L, Yan C, Ma Z, Grinter SZ, Zou X.
    Proteins; 2017 Mar 24; 85(3):424-434. PubMed ID: 27802576
    [Abstract] [Full Text] [Related]

  • 18. Molecular docking with ligand attached water molecules.
    Lie MA, Thomsen R, Pedersen CN, Schiøtt B, Christensen MH.
    J Chem Inf Model; 2011 Apr 25; 51(4):909-17. PubMed ID: 21452852
    [Abstract] [Full Text] [Related]

  • 19. 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]

  • 20. Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015.
    Slynko I, Da Silva F, Bret G, Rognan D.
    J Comput Aided Mol Des; 2016 Sep 30; 30(9):669-683. PubMed ID: 27480696
    [Abstract] [Full Text] [Related]

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