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Journal Abstract Search

165 related items for PubMed ID: 32835483

  • 1. 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]

  • 2. Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module.
    Pool R, Heringa J, Hoefling M, Schulz R, Smith JC, Feenstra KA.
    J Comput Chem; 2012 May 05; 33(12):1207-14. PubMed ID: 22370965
    [Abstract] [Full Text] [Related]

  • 3. 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]

  • 4. 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 09; 36(10):767-779. PubMed ID: 36198874
    [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. 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 08; 35(2):167-177. PubMed ID: 32968887
    [Abstract] [Full Text] [Related]

  • 7. 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]

  • 8. 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]

  • 9. 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]

  • 10. 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]

  • 11. 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]

  • 12. Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses.
    Lukauskis D, Samways ML, Aureli S, Cossins BP, Taylor RD, Gervasio FL.
    J Chem Inf Model; 2022 Dec 12; 62(23):6209-6216. PubMed ID: 36401553
    [Abstract] [Full Text] [Related]

  • 13. Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo.
    Ross GA, Bodnarchuk MS, Essex JW.
    J Am Chem Soc; 2015 Dec 02; 137(47):14930-43. PubMed ID: 26509924
    [Abstract] [Full Text] [Related]

  • 14. 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]

  • 15. Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies.
    Resat H, Marrone TJ, McCammon JA.
    Biophys J; 1997 Feb 12; 72(2 Pt 1):522-32. PubMed ID: 9017183
    [Abstract] [Full Text] [Related]

  • 16. Grand canonical Monte Carlo simulations of water in protein environments.
    Woo HJ, Dinner AR, Roux B.
    J Chem Phys; 2004 Oct 01; 121(13):6392-400. PubMed ID: 15446937
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  • 17. Grand canonical Monte Carlo simulation of ligand-protein binding.
    Clark M, Guarnieri F, Shkurko I, Wiseman J.
    J Chem Inf Model; 2006 Oct 01; 46(1):231-42. PubMed ID: 16426059
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  • 18. Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.
    Resat H, Mezei M.
    Biophys J; 1996 Sep 01; 71(3):1179-90. PubMed ID: 8873992
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  • 19. Molecular exchange Monte Carlo: A generalized method for identity exchanges in grand canonical Monte Carlo simulations.
    Soroush Barhaghi M, Torabi K, Nejahi Y, Schwiebert L, Potoff JJ.
    J Chem Phys; 2018 Aug 21; 149(7):072318. PubMed ID: 30134670
    [Abstract] [Full Text] [Related]

  • 20. Grand-canonical molecular dynamics simulations powered by a hybrid 4D nonequilibrium MD/MC method: Implementation in LAMMPS and applications to electrolyte solutions.
    Kim J, Belloni L, Rotenberg B.
    J Chem Phys; 2023 Oct 14; 159(14):. PubMed ID: 37819001
    [Abstract] [Full Text] [Related]

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