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Journal Abstract Search

155 related items for PubMed ID: 28911225

  • 1. 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]

  • 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 12; 36(10):767-779. PubMed ID: 36198874
    [Abstract] [Full Text] [Related]

  • 3. Capturing the energetics of water insertion in biological systems: the water flooding approach.
    Chakrabarty S, Warshel A.
    Proteins; 2013 Jan 12; 81(1):93-106. PubMed ID: 22911614
    [Abstract] [Full Text] [Related]

  • 4. 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]

  • 5. 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]

  • 6. 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
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  • 8. 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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  • 10. 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
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  • 12. Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo.
    Ross GA, Bruce Macdonald HE, Cave-Ayland C, Cabedo Martinez AI, Essex JW.
    J Chem Theory Comput; 2017 Dec 12; 13(12):6373-6381. PubMed ID: 29091438
    [Abstract] [Full Text] [Related]

  • 13. Molecular simulations of water and paracresol in MFI zeolite--a Monte Carlo study.
    Narasimhan L, Boulet P, Kuchta B, Schaef O, Denoyel R, Brunet P.
    Langmuir; 2009 Oct 06; 25(19):11598-607. PubMed ID: 19711959
    [Abstract] [Full Text] [Related]

  • 14. 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]

  • 15. 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
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  • 17. Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.
    Resat H, Mezei M.
    Biophys J; 1996 Sep 26; 71(3):1179-90. PubMed ID: 8873992
    [Abstract] [Full Text] [Related]

  • 18. 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]

  • 19. Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study.
    Korolev N, Lyubartsev AP, Nordenskiöld L, Laaksonen A.
    J Mol Biol; 2001 May 18; 308(5):907-17. PubMed ID: 11352581
    [Abstract] [Full Text] [Related]

  • 20. MPEXS-DNA, a new GPU-based Monte Carlo simulator for track structures and radiation chemistry at subcellular scale.
    Okada S, Murakami K, Incerti S, Amako K, Sasaki T.
    Med Phys; 2019 Mar 18; 46(3):1483-1500. PubMed ID: 30593679
    [Abstract] [Full Text] [Related]

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