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Journal Abstract Search

428 related items for PubMed ID: 29785435

  • 21. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI).
    Su PC, Tsai CC, Mehboob S, Hevener KE, Johnson ME.
    J Comput Chem; 2015 Sep 30; 36(25):1859-73. PubMed ID: 26216222
    [Abstract] [Full Text] [Related]

  • 22. Interaction Entropy for Computational Alanine Scanning.
    Yan Y, Yang M, Ji CG, Zhang JZH.
    J Chem Inf Model; 2017 May 22; 57(5):1112-1122. PubMed ID: 28406301
    [Abstract] [Full Text] [Related]

  • 23. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.
    Rastelli G, Del Rio A, Degliesposti G, Sgobba M.
    J Comput Chem; 2010 Mar 22; 31(4):797-810. PubMed ID: 19569205
    [Abstract] [Full Text] [Related]

  • 24. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
    Genheden S, Ryde U.
    Proteins; 2012 May 22; 80(5):1326-42. PubMed ID: 22274991
    [Abstract] [Full Text] [Related]

  • 25. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
    Genheden S, Ryde U.
    Expert Opin Drug Discov; 2015 May 22; 10(5):449-61. PubMed ID: 25835573
    [Abstract] [Full Text] [Related]

  • 26. Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method.
    Sun Y, He X, Hou T, Cai L, Man VH, Wang J.
    J Comput Chem; 2023 May 30; 44(14):1334-1346. PubMed ID: 36807356
    [Abstract] [Full Text] [Related]

  • 27. How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?
    Hao D, He X, Ji B, Zhang S, Wang J.
    J Chem Inf Model; 2020 Dec 28; 60(12):6624-6633. PubMed ID: 33213150
    [Abstract] [Full Text] [Related]

  • 28. Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses.
    Yu Y, Wang Z, Wang L, Tian S, Hou T, Sun H.
    J Cheminform; 2022 Aug 20; 14(1):56. PubMed ID: 35987841
    [Abstract] [Full Text] [Related]

  • 29. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
    Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T.
    Chem Rev; 2019 Aug 28; 119(16):9478-9508. PubMed ID: 31244000
    [Abstract] [Full Text] [Related]

  • 30. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking.
    Hou T, Wang J, Li Y, Wang W.
    J Comput Chem; 2011 Apr 15; 32(5):866-77. PubMed ID: 20949517
    [Abstract] [Full Text] [Related]

  • 31. Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method.
    Zhong S, Huang K, Luo S, Dong S, Duan L.
    Phys Chem Chem Phys; 2020 Feb 19; 22(7):4240-4251. PubMed ID: 32043094
    [Abstract] [Full Text] [Related]

  • 32. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters.
    Wang J, Shao Q, Cossins BP, Shi J, Chen K, Zhu W.
    J Biomol Struct Dyn; 2016 Feb 19; 34(1):163-76. PubMed ID: 25761118
    [Abstract] [Full Text] [Related]

  • 33. The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction.
    Li Y, Cong Y, Feng G, Zhong S, Zhang JZH, Sun H, Duan L.
    Struct Dyn; 2018 Nov 19; 5(6):064101. PubMed ID: 30868080
    [Abstract] [Full Text] [Related]

  • 34. Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities.
    Wang E, Liu H, Wang J, Weng G, Sun H, Wang Z, Kang Y, Hou T.
    J Chem Inf Model; 2020 Nov 23; 60(11):5353-5365. PubMed ID: 32175734
    [Abstract] [Full Text] [Related]

  • 35. Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.
    Zoete V, Michielin O.
    Proteins; 2007 Jun 01; 67(4):1026-47. PubMed ID: 17377991
    [Abstract] [Full Text] [Related]

  • 36. Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.
    Wickstrom L, Gallicchio E, Chen L, Kurtzman T, Deng N.
    Phys Chem Chem Phys; 2022 Mar 09; 24(10):6037-6052. PubMed ID: 35212338
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  • 37. Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures.
    Yau MQ, Emtage AL, Chan NJY, Doughty SW, Loo JSE.
    J Comput Aided Mol Des; 2019 May 09; 33(5):487-496. PubMed ID: 30989574
    [Abstract] [Full Text] [Related]

  • 38. Simple Entropy Terms for End-Point Binding Free Energy Calculations.
    Menzer WM, Li C, Sun W, Xie B, Minh DDL.
    J Chem Theory Comput; 2018 Nov 13; 14(11):6035-6049. PubMed ID: 30296084
    [Abstract] [Full Text] [Related]

  • 39. Computational Alanine Scanning with Interaction Entropy for Protein-Ligand Binding Free Energies.
    Liu X, Peng L, Zhou Y, Zhang Y, Zhang JZH.
    J Chem Theory Comput; 2018 Mar 13; 14(3):1772-1780. PubMed ID: 29406753
    [Abstract] [Full Text] [Related]

  • 40. Binding Free Energies of Conformationally Disordered Peptides Through Extensive Sampling and End-Point Methods.
    Nixon MG, Fadda E.
    Methods Mol Biol; 2019 Mar 13; 2039():229-242. PubMed ID: 31342430
    [Abstract] [Full Text] [Related]

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