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Journal Abstract Search

149 related items for PubMed ID: 35637786

  • 1. 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]

  • 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 25; 36(10):767-779. PubMed ID: 36198874
    [Abstract] [Full Text] [Related]

  • 3. 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]

  • 4. 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]

  • 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. 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]

  • 7. 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]

  • 8. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.
    Nguyen CN, Young TK, Gilson MK.
    J Chem Phys; 2012 Jul 28; 137(4):044101. PubMed ID: 22852591
    [Abstract] [Full Text] [Related]

  • 9. 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]

  • 10. 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]

  • 11. 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]

  • 12. 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]

  • 13. 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]

  • 14. 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]

  • 15. 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]

  • 16. 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 Feb 14; 23(2):128-41. PubMed ID: 20151411
    [Abstract] [Full Text] [Related]

  • 17. AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.
    Uehara S, Tanaka S.
    Molecules; 2016 Nov 23; 21(11):. PubMed ID: 27886114
    [Abstract] [Full Text] [Related]

  • 18. Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory.
    Chen L, Cruz A, Roe DR, Simmonett AC, Wickstrom L, Deng N, Kurtzman T.
    J Chem Theory Comput; 2021 May 11; 17(5):2714-2724. PubMed ID: 33830762
    [Abstract] [Full Text] [Related]

  • 19. Water Networks in Complexes between Proteins and FDA-Approved Drugs.
    Samways ML, Bruce Macdonald HE, Taylor RD, Essex JW.
    J Chem Inf Model; 2023 Jan 09; 63(1):387-396. PubMed ID: 36469670
    [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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