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Journal Abstract Search

652 related items for PubMed ID: 21554075

  • 41. A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming.
    Amini A, Shrimpton PJ, Muggleton SH, Sternberg MJ.
    Proteins; 2007 Dec 01; 69(4):823-31. PubMed ID: 17910057
    [Abstract] [Full Text] [Related]

  • 42. Towards predictive ligand design with free-energy based computational methods?
    Foloppe N, Hubbard R.
    Curr Med Chem; 2006 Dec 01; 13(29):3583-608. PubMed ID: 17168725
    [Abstract] [Full Text] [Related]

  • 43. Machine learning in computational docking.
    Khamis MA, Gomaa W, Ahmed WF.
    Artif Intell Med; 2015 Mar 01; 63(3):135-52. PubMed ID: 25724101
    [Abstract] [Full Text] [Related]

  • 44. Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.
    van Lipzig MM, ter Laak AM, Jongejan A, Vermeulen NP, Wamelink M, Geerke D, Meerman JH.
    J Med Chem; 2004 Feb 12; 47(4):1018-30. PubMed ID: 14761204
    [Abstract] [Full Text] [Related]

  • 45. Supervised scoring models with docked ligand conformations for structure-based virtual screening.
    Teramoto R, Fukunishi H.
    J Chem Inf Model; 2007 Feb 12; 47(5):1858-67. PubMed ID: 17685604
    [Abstract] [Full Text] [Related]

  • 46. 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]

  • 47. Calculation of affinities of peptides for proteins.
    Donnini S, Juffer AH.
    J Comput Chem; 2004 Feb 07; 25(3):393-411. PubMed ID: 14696074
    [Abstract] [Full Text] [Related]

  • 48. General and targeted statistical potentials for protein-ligand interactions.
    Mooij WT, Verdonk ML.
    Proteins; 2005 Nov 01; 61(2):272-87. PubMed ID: 16106379
    [Abstract] [Full Text] [Related]

  • 49. A novel empirical free energy function that explains and predicts protein-protein binding affinities.
    Audie J, Scarlata S.
    Biophys Chem; 2007 Sep 01; 129(2-3):198-211. PubMed ID: 17600612
    [Abstract] [Full Text] [Related]

  • 50. Quantum-Mechanics Methodologies in Drug Discovery: Applications of Docking and Scoring in Lead Optimization.
    Crespo A, Rodriguez-Granillo A, Lim VT.
    Curr Top Med Chem; 2017 Sep 01; 17(23):2663-2680. PubMed ID: 28685695
    [Abstract] [Full Text] [Related]

  • 51. A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase.
    Steinbrecher T, Case DA, Labahn A.
    J Med Chem; 2006 Mar 23; 49(6):1837-44. PubMed ID: 16539369
    [Abstract] [Full Text] [Related]

  • 52. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.
    Cournia Z, Allen B, Sherman W.
    J Chem Inf Model; 2017 Dec 26; 57(12):2911-2937. PubMed ID: 29243483
    [Abstract] [Full Text] [Related]

  • 53. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.
    Taylor RD, Jewsbury PJ, Essex JW.
    J Comput Chem; 2003 Oct 26; 24(13):1637-56. PubMed ID: 12926007
    [Abstract] [Full Text] [Related]

  • 54. Recent advances in the development and application of implicit solvent models in biomolecule simulations.
    Feig M, Brooks CL.
    Curr Opin Struct Biol; 2004 Apr 26; 14(2):217-24. PubMed ID: 15093837
    [Abstract] [Full Text] [Related]

  • 55. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.
    Ryde U, Söderhjelm P.
    Chem Rev; 2016 May 11; 116(9):5520-66. PubMed ID: 27077817
    [Abstract] [Full Text] [Related]

  • 56. Explicit Drug Re-positioning: Predicting Novel Drug-Target Interactions of the Shelved Molecules with QM/MM Based Approaches.
    Omer A, Suryanarayanan V, Selvaraj C, Singh SK, Singh P.
    Adv Protein Chem Struct Biol; 2015 May 11; 100():89-112. PubMed ID: 26415842
    [Abstract] [Full Text] [Related]

  • 57.
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  • 58. HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.
    Floriano WB, Vaidehi N, Zamanakos G, Goddard WA.
    J Med Chem; 2004 Jan 01; 47(1):56-71. PubMed ID: 14695820
    [Abstract] [Full Text] [Related]

  • 59. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
    Riccardi D, Schaefer P, Cui Q.
    J Phys Chem B; 2005 Sep 22; 109(37):17715-33. PubMed ID: 16853267
    [Abstract] [Full Text] [Related]

  • 60.
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