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Journal Abstract Search

218 related items for PubMed ID: 30640456

  • 1. Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules.
    Wahl J, Smieško M.
    J Chem Inf Model; 2019 Feb 25; 59(2):754-765. PubMed ID: 30640456
    [Abstract] [Full Text] [Related]

  • 2. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.
    Deng Y, Roux B.
    J Chem Phys; 2008 Mar 21; 128(11):115103. PubMed ID: 18361618
    [Abstract] [Full Text] [Related]

  • 3. Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo.
    Ross GA, Russell E, Deng Y, Lu C, Harder ED, Abel R, Wang L.
    J Chem Theory Comput; 2020 Oct 13; 16(10):6061-6076. PubMed ID: 32955877
    [Abstract] [Full Text] [Related]

  • 4. 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]

  • 5. Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome.
    Ge X, Roux B.
    J Phys Chem B; 2010 Jul 29; 114(29):9525-39. PubMed ID: 20608691
    [Abstract] [Full Text] [Related]

  • 6. Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.
    Ben-Shalom IY, Lin Z, Radak BK, Lin C, Sherman W, Gilson MK.
    J Chem Theory Comput; 2020 Dec 08; 16(12):7883-7894. PubMed ID: 33206520
    [Abstract] [Full Text] [Related]

  • 7. Accelerating Convergence of Free Energy Computations with Hamiltonian Simulated Annealing of Solvent (HSAS).
    Jiang W.
    J Chem Theory Comput; 2019 Apr 09; 15(4):2179-2186. PubMed ID: 30821969
    [Abstract] [Full Text] [Related]

  • 8. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.
    Misini Ignjatović M, Caldararu O, Dong G, Muñoz-Gutierrez C, Adasme-Carreño F, Ryde U.
    J Comput Aided Mol Des; 2016 Sep 09; 30(9):707-730. PubMed ID: 27565797
    [Abstract] [Full Text] [Related]

  • 9. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L, Chambers J, Abel R.
    Methods Mol Biol; 2019 Sep 09; 2022():201-232. PubMed ID: 31396905
    [Abstract] [Full Text] [Related]

  • 10. Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields.
    Deng J, Cui Q.
    J Chem Theory Comput; 2024 Mar 12; 20(5):1897-1911. PubMed ID: 38417108
    [Abstract] [Full Text] [Related]

  • 11. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
    Ge X, Roux B.
    J Mol Recognit; 2010 Mar 12; 23(2):128-41. PubMed ID: 20151411
    [Abstract] [Full Text] [Related]

  • 12. Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.
    Ge Y, Melling OJ, Dong W, Essex JW, Mobley DL.
    J Comput Aided Mol Des; 2022 Oct 12; 36(10):767-779. PubMed ID: 36198874
    [Abstract] [Full Text] [Related]

  • 13. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.
    Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U.
    J Am Chem Soc; 2011 Aug 24; 133(33):13081-92. PubMed ID: 21728337
    [Abstract] [Full Text] [Related]

  • 14. Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.
    Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL.
    J Chem Theory Comput; 2022 Mar 08; 18(3):1359-1381. PubMed ID: 35148093
    [Abstract] [Full Text] [Related]

  • 15. Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes.
    Huggins DJ, Payne MC.
    J Phys Chem B; 2013 Jul 11; 117(27):8232-44. PubMed ID: 23763625
    [Abstract] [Full Text] [Related]

  • 16. Strategies to calculate water binding free energies in protein-ligand complexes.
    Bodnarchuk MS, Viner R, Michel J, Essex JW.
    J Chem Inf Model; 2014 Jun 23; 54(6):1623-33. PubMed ID: 24684745
    [Abstract] [Full Text] [Related]

  • 17. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.
    Katkova EV, Onufriev AV, Aguilar B, Sulimov VB.
    J Mol Graph Model; 2017 Mar 23; 72():70-80. PubMed ID: 28064081
    [Abstract] [Full Text] [Related]

  • 18. Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo.
    Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL.
    J Comput Aided Mol Des; 2021 Feb 23; 35(2):167-177. PubMed ID: 32968887
    [Abstract] [Full Text] [Related]

  • 19. Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations.
    Wahl J, Smieško M.
    ChemMedChem; 2018 Jul 06; 13(13):1325-1335. PubMed ID: 29726604
    [Abstract] [Full Text] [Related]

  • 20. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions.
    Hori K, Yamaguchi T, Uezu K, Sumimoto M.
    J Comput Chem; 2011 Apr 15; 32(5):778-86. PubMed ID: 21341291
    [Abstract] [Full Text] [Related]

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