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Journal Abstract Search

267 related items for PubMed ID: 38147689

  • 1. Tuning Potential Functions to Host-Guest Binding Data.
    Setiadi J, Boothroyd S, Slochower DR, Dotson DL, Thompson MW, Wagner JR, Wang LP, Gilson MK.
    J Chem Theory Comput; 2024 Jan 09; 20(1):239-252. PubMed ID: 38147689
    [Abstract] [Full Text] [Related]

  • 2. Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.
    Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson MK.
    J Chem Theory Comput; 2019 Nov 12; 15(11):6225-6242. PubMed ID: 31603667
    [Abstract] [Full Text] [Related]

  • 3. 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 12; 72():70-80. PubMed ID: 28064081
    [Abstract] [Full Text] [Related]

  • 4. Overview of the SAMPL5 host-guest challenge: Are we doing better?
    Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK.
    J Comput Aided Mol Des; 2017 Jan 12; 31(1):1-19. PubMed ID: 27658802
    [Abstract] [Full Text] [Related]

  • 5. Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes.
    Zhang H, Yin C, Yan H, van der Spoel D.
    J Chem Inf Model; 2016 Oct 24; 56(10):2080-2092. PubMed ID: 27626790
    [Abstract] [Full Text] [Related]

  • 6. Overview of the SAMPL6 host-guest binding affinity prediction challenge.
    Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD.
    J Comput Aided Mol Des; 2018 Oct 24; 32(10):937-963. PubMed ID: 30415285
    [Abstract] [Full Text] [Related]

  • 7. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).
    Caldararu O, Olsson MA, Riplinger C, Neese F, Ryde U.
    J Comput Aided Mol Des; 2017 Jan 24; 31(1):87-106. PubMed ID: 27600554
    [Abstract] [Full Text] [Related]

  • 8. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.
    Yin J, Henriksen NM, Slochower DR, Gilson MK.
    J Comput Aided Mol Des; 2017 Jan 24; 31(1):133-145. PubMed ID: 27638809
    [Abstract] [Full Text] [Related]

  • 9. Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach.
    Liu HY, Zou X.
    J Phys Chem B; 2006 May 11; 110(18):9304-13. PubMed ID: 16671749
    [Abstract] [Full Text] [Related]

  • 10. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.
    Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM.
    J Mol Recognit; 2016 Jan 11; 29(1):10-21. PubMed ID: 26256816
    [Abstract] [Full Text] [Related]

  • 11. Rapid alchemical free energy calculation employing a generalized born implicit solvent model.
    Ostermeir K, Zacharias M.
    J Phys Chem B; 2015 Jan 22; 119(3):968-75. PubMed ID: 25160060
    [Abstract] [Full Text] [Related]

  • 12. A Physics-Guided Neural Network for Predicting Protein-Ligand Binding Free Energy: From Host-Guest Systems to the PDBbind Database.
    Cain S, Risheh A, Forouzesh N.
    Biomolecules; 2022 Jun 29; 12(7):. PubMed ID: 35883475
    [Abstract] [Full Text] [Related]

  • 13. Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.
    Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson MK.
    J Comput Aided Mol Des; 2012 May 29; 26(5):475-87. PubMed ID: 22366955
    [Abstract] [Full Text] [Related]

  • 14. Multiscale generalized born modeling of ligand binding energies for virtual database screening.
    Liu HY, Grinter SZ, Zou X.
    J Phys Chem B; 2009 Sep 03; 113(35):11793-9. PubMed ID: 19678651
    [Abstract] [Full Text] [Related]

  • 15. 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]

  • 16. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.
    Liu X, Zheng L, Cong Y, Gong Z, Yin Z, Zhang JZH, Liu Z, Sun Z.
    J Comput Aided Mol Des; 2022 Dec 08; 36(12):879-894. PubMed ID: 36394776
    [Abstract] [Full Text] [Related]

  • 17. Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
    Lee J, Tofoleanu F, Pickard FC, König G, Huang J, Damjanović A, Baek M, Seok C, Brooks BR.
    J Comput Aided Mol Des; 2017 Jan 08; 31(1):71-85. PubMed ID: 27677749
    [Abstract] [Full Text] [Related]

  • 18. Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization.
    Zhang H, Tan T, van der Spoel D.
    J Chem Theory Comput; 2015 Nov 10; 11(11):5103-13. PubMed ID: 26574308
    [Abstract] [Full Text] [Related]

  • 19. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.
    Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C.
    J Phys Chem B; 2007 Feb 22; 111(7):1846-57. PubMed ID: 17256983
    [Abstract] [Full Text] [Related]

  • 20. A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.
    Yamagishi J, Okimoto N, Morimoto G, Taiji M.
    J Comput Chem; 2014 Nov 05; 35(29):2132-9. PubMed ID: 25220475
    [Abstract] [Full Text] [Related]

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