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Journal Abstract Search

283 related items for PubMed ID: 29486559

  • 1. 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]

  • 2. 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 31; 35(2):167-177. PubMed ID: 32968887
    [Abstract] [Full Text] [Related]

  • 3. Reversibly Sampling Conformations and Binding Modes Using Molecular Darting.
    Gill SC, Mobley DL.
    J Chem Theory Comput; 2021 Jan 12; 17(1):302-314. PubMed ID: 33289558
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  • 4. 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
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  • 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
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  • 6. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.
    Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L.
    J Chem Theory Comput; 2015 Jun 09; 11(6):2670-9. PubMed ID: 26085821
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  • 7. Grand canonical Monte Carlo simulation of ligand-protein binding.
    Clark M, Guarnieri F, Shkurko I, Wiseman J.
    J Chem Inf Model; 2006 Jun 09; 46(1):231-42. PubMed ID: 16426059
    [Abstract] [Full Text] [Related]

  • 8. 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
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  • 12. Receptor-Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method.
    Liu H, Deng J, Luo Z, Lin Y, Merz KM, Zheng Z.
    J Chem Theory Comput; 2020 Oct 13; 16(10):6645-6655. PubMed ID: 32857938
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  • 14. Perspective: Alchemical free energy calculations for drug discovery.
    Mobley DL, Klimovich PV.
    J Chem Phys; 2012 Dec 21; 137(23):230901. PubMed ID: 23267463
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  • 15. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.
    Kaus JW, McCammon JA.
    J Phys Chem B; 2015 May 21; 119(20):6190-7. PubMed ID: 25906170
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  • 16. Sensitivity in Binding Free Energies Due to Protein Reorganization.
    Lim NM, Wang L, Abel R, Mobley DL.
    J Chem Theory Comput; 2016 Sep 13; 12(9):4620-31. PubMed ID: 27462935
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  • 17. Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations.
    Baumann HM, Gapsys V, de Groot BL, Mobley DL.
    J Phys Chem B; 2021 May 06; 125(17):4241-4261. PubMed ID: 33905257
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  • 18. Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein-Ligand Sampling.
    Liu W, Liu Z, Liu H, Westerhoff LM, Zheng Z.
    J Chem Inf Model; 2022 Nov 28; 62(22):5645-5665. PubMed ID: 36282990
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