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Journal Abstract Search

130 related items for PubMed ID: 30821969

  • 1. 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
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  • 6. 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
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  • 7. 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
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  • 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
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  • 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
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  • 12. Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics.
    Jiang W.
    J Chem Theory Comput; 2024 Apr 23; 20(8):3085-3095. PubMed ID: 38568961
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  • 13. Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).
    Jiang W, Hodoscek M, Roux B.
    J Chem Theory Comput; 2009 Oct 01; 5(10):2583-2588. PubMed ID: 21857812
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  • 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
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  • 15. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.
    Wang J, Deng Y, Roux B.
    Biophys J; 2006 Oct 15; 91(8):2798-814. PubMed ID: 16844742
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  • 16. 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
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  • 17. 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
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  • 18. 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
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  • 19. 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
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  • 20. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.
    Shivakumar D, Deng Y, Roux B.
    J Chem Theory Comput; 2009 Apr 14; 5(4):919-30. PubMed ID: 26609601
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