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Journal Abstract Search

206 related items for PubMed ID: 21735452

  • 1. Surveying implicit solvent models for estimating small molecule absolute hydration free energies.
    Knight JL, Brooks CL.
    J Comput Chem; 2011 Oct; 32(13):2909-23. PubMed ID: 21735452
    [Abstract] [Full Text] [Related]

  • 2. Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.
    Knight JL, Yesselman JD, Brooks CL.
    J Comput Chem; 2013 Apr 30; 34(11):893-903. PubMed ID: 23292859
    [Abstract] [Full Text] [Related]

  • 3. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.
    Mobley DL, Dumont E, Chodera JD, Dill KA.
    J Phys Chem B; 2007 Mar 08; 111(9):2242-54. PubMed ID: 17291029
    [Abstract] [Full Text] [Related]

  • 4. 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
    [Abstract] [Full Text] [Related]

  • 5. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.
    Katkova EV, Onufriev AV, Aguilar B, Sulimov VB.
    J Mol Graph Model; 2017 Mar 14; 72():70-80. PubMed ID: 28064081
    [Abstract] [Full Text] [Related]

  • 6. Explicit Solvent Hydration Benchmark for Proteins with Application to the PBSA Method.
    Setny P, Dudek A.
    J Chem Theory Comput; 2017 Jun 13; 13(6):2762-2776. PubMed ID: 28498675
    [Abstract] [Full Text] [Related]

  • 7. Generalized Born implicit solvent models for small molecule hydration free energies.
    Brieg M, Setzler J, Albert S, Wenzel W.
    Phys Chem Chem Phys; 2017 Jan 04; 19(2):1677-1685. PubMed ID: 27995260
    [Abstract] [Full Text] [Related]

  • 8. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.
    Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W.
    J Chem Theory Comput; 2010 May 11; 6(5):1509-19. PubMed ID: 26615687
    [Abstract] [Full Text] [Related]

  • 9. Treating entropy and conformational changes in implicit solvent simulations of small molecules.
    Mobley DL, Dill KA, Chodera JD.
    J Phys Chem B; 2008 Jan 24; 112(3):938-46. PubMed ID: 18171044
    [Abstract] [Full Text] [Related]

  • 10. 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 24; 34(5):543-560. PubMed ID: 31960254
    [Abstract] [Full Text] [Related]

  • 11. Comparative Assessment of Computational Methods for Free Energy Calculations of Ionic Hydration.
    Zhang H, Jiang Y, Yan H, Cui Z, Yin C.
    J Chem Inf Model; 2017 Nov 27; 57(11):2763-2775. PubMed ID: 29039666
    [Abstract] [Full Text] [Related]

  • 12. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.
    Izadi S, Aguilar B, Onufriev AV.
    J Chem Theory Comput; 2015 Sep 08; 11(9):4450-9. PubMed ID: 26575935
    [Abstract] [Full Text] [Related]

  • 13. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.
    Aleksandrov A, Lin FY, Roux B, MacKerell AD.
    J Comput Chem; 2018 Aug 15; 39(22):1707-1719. PubMed ID: 29737546
    [Abstract] [Full Text] [Related]

  • 14. The effects of implicit modeling of nonpolar solvation on protein folding simulations.
    Shao Q, Zhu W.
    Phys Chem Chem Phys; 2018 Jul 11; 20(27):18410-18419. PubMed ID: 29946610
    [Abstract] [Full Text] [Related]

  • 15. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
    Deng N, Zhang BW, Levy RM.
    J Chem Theory Comput; 2015 Jun 09; 11(6):2868-78. PubMed ID: 26236174
    [Abstract] [Full Text] [Related]

  • 16. Hydration in discrete water (II): from neutral to charged solutes.
    Setny P.
    J Phys Chem B; 2015 May 14; 119(19):5970-8. PubMed ID: 25896299
    [Abstract] [Full Text] [Related]

  • 17. FreeSolv: a database of experimental and calculated hydration free energies, with input files.
    Mobley DL, Guthrie JP.
    J Comput Aided Mol Des; 2014 Jul 14; 28(7):711-20. PubMed ID: 24928188
    [Abstract] [Full Text] [Related]

  • 18. Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.
    Lara A, Riquelme M, Vöhringer-Martinez E.
    J Comput Chem; 2018 Aug 15; 39(22):1728-1737. PubMed ID: 29752734
    [Abstract] [Full Text] [Related]

  • 19. Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4.
    König G, Pickard FC, Mei Y, Brooks BR.
    J Comput Aided Mol Des; 2014 Mar 15; 28(3):245-57. PubMed ID: 24504703
    [Abstract] [Full Text] [Related]

  • 20. Blind prediction of solvation free energies from the SAMPL4 challenge.
    Mobley DL, Wymer KL, Lim NM, Guthrie JP.
    J Comput Aided Mol Des; 2014 Mar 15; 28(3):135-50. PubMed ID: 24615156
    [Abstract] [Full Text] [Related]

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