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Journal Abstract Search

255 related items for PubMed ID: 33206520

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

  • 2. Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units.
    Ben-Shalom IY, Lin C, Radak BK, Sherman W, Gilson MK.
    J Chem Theory Comput; 2021 Dec 14; 17(12):7366-7372. PubMed ID: 34762421
    [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 14; 35(2):167-177. PubMed ID: 32968887
    [Abstract] [Full Text] [Related]

  • 4. Simulating Water Exchange to Buried Binding Sites.
    Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK.
    J Chem Theory Comput; 2019 Apr 09; 15(4):2684-2691. PubMed ID: 30835999
    [Abstract] [Full Text] [Related]

  • 5. 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]

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  • 7. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L, Chambers J, Abel R.
    Methods Mol Biol; 2019 Feb 25; 2022():201-232. PubMed ID: 31396905
    [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. 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]

  • 10. 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]

  • 11. Absolute Binding Free Energy Calculations for Buried Water Molecules.
    Ge Y, Baumann HM, Mobley DL.
    J Chem Theory Comput; 2022 Nov 08; 18(11):6482-6499. PubMed ID: 36197451
    [Abstract] [Full Text] [Related]

  • 12. Dissecting the Influence of Protein Flexibility on the Location and Thermodynamic Profile of Explicit Water Molecules in Protein-Ligand Binding.
    Yang Y, Lill MA.
    J Chem Theory Comput; 2016 Sep 13; 12(9):4578-92. PubMed ID: 27494046
    [Abstract] [Full Text] [Related]

  • 13. 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 13; 36(10):767-779. PubMed ID: 36198874
    [Abstract] [Full Text] [Related]

  • 14. 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]

  • 15. 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]

  • 16. 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
    [Abstract] [Full Text] [Related]

  • 17. Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields.
    Fan S, Iorga BI, Beckstein O.
    J Comput Aided Mol Des; 2020 May 23; 34(5):543-560. PubMed ID: 31960254
    [Abstract] [Full Text] [Related]

  • 18. Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc.
    Ariz-Extreme I, Hub JS.
    PLoS One; 2018 May 23; 13(5):e0196751. PubMed ID: 29771936
    [Abstract] [Full Text] [Related]

  • 19. Hydration energy landscape of the active site cavity in cytochrome P450cam.
    Helms V, Wade RC.
    Proteins; 1998 Aug 15; 32(3):381-96. PubMed ID: 9715913
    [Abstract] [Full Text] [Related]

  • 20. Calculation of Thermodynamic Properties of Bound Water Molecules.
    Yang Y, Abdallah AHA, Lill MA.
    Methods Mol Biol; 2018 Aug 15; 1762():389-402. PubMed ID: 29594782
    [Abstract] [Full Text] [Related]

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