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Journal Abstract Search

153 related items for PubMed ID: 36198874

  • 1. 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; 36(10):767-779. PubMed ID: 36198874
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo.
    Melling OJ, Samways ML, Ge Y, Mobley DL, Essex JW.
    J Chem Theory Comput; 2023 Feb 14; 19(3):1050-1062. PubMed ID: 36692215
    [Abstract] [Full Text] [Related]

  • 4. 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 14; 35(2):167-177. PubMed ID: 32968887
    [Abstract] [Full Text] [Related]

  • 5. 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]

  • 6. 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]

  • 7. 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]

  • 8. 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]

  • 9. 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]

  • 10. Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water.
    Sun D, Lakkaraju SK, Jo S, MacKerell AD.
    J Chem Theory Comput; 2018 Oct 09; 14(10):5290-5302. PubMed ID: 30183291
    [Abstract] [Full Text] [Related]

  • 11. Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations.
    Lakkaraju SK, Raman EP, Yu W, MacKerell AD.
    J Chem Theory Comput; 2014 Jun 10; 10(6):2281-2290. PubMed ID: 24932136
    [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. GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations.
    Zhao M, Kognole AA, Jo S, Tao A, Hazel A, MacKerell AD.
    J Comput Chem; 2023 Jul 30; 44(20):1719-1732. PubMed ID: 37093676
    [Abstract] [Full Text] [Related]

  • 14. Impact of ribosomal modification on the binding of the antibiotic telithromycin using a combined grand canonical monte carlo/molecular dynamics simulation approach.
    Small MC, Lopes P, Andrade RB, Mackerell AD.
    PLoS Comput Biol; 2013 Jul 30; 9(6):e1003113. PubMed ID: 23785274
    [Abstract] [Full Text] [Related]

  • 15. 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]

  • 16. 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]

  • 17. Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations.
    Yoon H, Kolev V, Warshel A.
    J Phys Chem B; 2017 Oct 12; 121(40):9358-9365. PubMed ID: 28911225
    [Abstract] [Full Text] [Related]

  • 18. Grand canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation (L8+) to the center of DNA oligomers.
    Olmsted MC, Bond JP, Anderson CF, Record MT.
    Biophys J; 1995 Feb 12; 68(2):634-47. PubMed ID: 7696515
    [Abstract] [Full Text] [Related]

  • 19. 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]

  • 20. Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics.
    Sasmal S, Gill SC, Lim NM, Mobley DL.
    J Chem Theory Comput; 2020 Mar 10; 16(3):1854-1865. PubMed ID: 32058713
    [Abstract] [Full Text] [Related]

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