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PUBMED FOR HANDHELDS

Journal Abstract Search


165 related items for PubMed ID: 32058713

  • 1. 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
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. 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]

  • 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 31; 36(10):767-779. PubMed ID: 36198874
    [Abstract] [Full Text] [Related]

  • 5. 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
    [Abstract] [Full Text] [Related]

  • 6. Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.
    Burley KH, Gill SC, Lim NM, Mobley DL.
    J Chem Theory Comput; 2019 Mar 12; 15(3):1848-1862. PubMed ID: 30677291
    [Abstract] [Full Text] [Related]

  • 7. Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.
    Lim NM, Osato M, Warren GL, Mobley DL.
    J Chem Theory Comput; 2020 Apr 14; 16(4):2778-2794. PubMed ID: 32167763
    [Abstract] [Full Text] [Related]

  • 8. 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]

  • 9. Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α.
    Spiriti J, Subramanian SR, Palli R, Wu M, Zuckerman DM.
    PLoS One; 2019 Mar 08; 14(4):e0215694. PubMed ID: 31013302
    [Abstract] [Full Text] [Related]

  • 10. 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
    [Abstract] [Full Text] [Related]

  • 11. 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
    [Abstract] [Full Text] [Related]

  • 12. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications.
    Reif MM, Zacharias M.
    J Chem Theory Comput; 2022 Jun 14; 18(6):3873-3893. PubMed ID: 35653503
    [Abstract] [Full Text] [Related]

  • 13. Binding Modes and Metabolism of Caffeine.
    Jandova Z, Gill SC, Lim NM, Mobley DL, Oostenbrink C.
    Chem Res Toxicol; 2019 Jul 15; 32(7):1374-1383. PubMed ID: 31132250
    [Abstract] [Full Text] [Related]

  • 14. Structural basis of binding of high-affinity ligands to protein kinase C: prediction of the binding modes through a new molecular dynamics method and evaluation by site-directed mutagenesis.
    Pak Y, Enyedy IJ, Varady J, Kung JW, Lorenzo PS, Blumberg PM, Wang S.
    J Med Chem; 2001 May 24; 44(11):1690-701. PubMed ID: 11356104
    [Abstract] [Full Text] [Related]

  • 15. 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
    [Abstract] [Full Text] [Related]

  • 16. Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand-Protein Recognition and Compound Design.
    Tang Z, Chen SH, Chang CA.
    J Chem Theory Comput; 2020 Mar 10; 16(3):1882-1895. PubMed ID: 32031801
    [Abstract] [Full Text] [Related]

  • 17. 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]

  • 18. 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
    [Abstract] [Full Text] [Related]

  • 19. New Monte Carlo Based Technique To Study DNA-Ligand Interactions.
    Cabeza de Vaca I, Lucas MF, Guallar V.
    J Chem Theory Comput; 2015 Dec 08; 11(12):5598-605. PubMed ID: 26642982
    [Abstract] [Full Text] [Related]

  • 20. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy.
    Wu Y, Brooks CL.
    J Chem Inf Model; 2021 Nov 22; 61(11):5535-5549. PubMed ID: 34704754
    [Abstract] [Full Text] [Related]


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