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Journal Abstract Search

164 related items for PubMed ID: 32955877

  • 1. 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]

  • 2. 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 13; 36(10):767-779. PubMed ID: 36198874
    [Abstract] [Full Text] [Related]

  • 3. 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]

  • 4. 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]

  • 5. 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]

  • 6. 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]

  • 7. 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]

  • 8. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L, Chambers J, Abel R.
    Methods Mol Biol; 2019 Jul 29; 2022():201-232. PubMed ID: 31396905
    [Abstract] [Full Text] [Related]

  • 9. 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 29; 35(2):167-177. PubMed ID: 32968887
    [Abstract] [Full Text] [Related]

  • 10. py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.
    Barhaghi MS, Crawford B, Schwing G, Hardy DJ, Stone JE, Schwiebert L, Potoff J, Tajkhorshid E.
    J Chem Theory Comput; 2022 Aug 09; 18(8):4983-4994. PubMed ID: 35621307
    [Abstract] [Full Text] [Related]

  • 11. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.
    Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL.
    J Phys Chem B; 2018 May 31; 122(21):5579-5598. PubMed ID: 29486559
    [Abstract] [Full Text] [Related]

  • 12. Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks.
    Ekberg V, Samways ML, Misini Ignjatović M, Essex JW, Ryde U.
    ACS Phys Chem Au; 2022 May 25; 2(3):247-259. PubMed ID: 35637786
    [Abstract] [Full Text] [Related]

  • 13. 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 May 25; 23(2):128-41. PubMed ID: 20151411
    [Abstract] [Full Text] [Related]

  • 14. 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]

  • 15. 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]

  • 16. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.
    Athanasiou C, Vasilakaki S, Dellis D, Cournia Z.
    J Comput Aided Mol Des; 2018 Jan 12; 32(1):21-44. PubMed ID: 29119352
    [Abstract] [Full Text] [Related]

  • 17. Relative Binding Free Energy Calculations Applied to Protein Homology Models.
    Cappel D, Hall ML, Lenselink EB, Beuming T, Qi J, Bradner J, Sherman W.
    J Chem Inf Model; 2016 Dec 27; 56(12):2388-2400. PubMed ID: 28024402
    [Abstract] [Full Text] [Related]

  • 18. 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]

  • 19. Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method.
    Oshima H, Re S, Sugita Y.
    J Chem Inf Model; 2020 Nov 23; 60(11):5382-5394. PubMed ID: 32786707
    [Abstract] [Full Text] [Related]

  • 20. grand: A Python Module for Grand Canonical Water Sampling in OpenMM.
    Samways ML, Bruce Macdonald HE, Essex JW.
    J Chem Inf Model; 2020 Oct 26; 60(10):4436-4441. PubMed ID: 32835483
    [Abstract] [Full Text] [Related]

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