Literature DB >> 24622881

Fast prediction of hydration free energies for SAMPL4 blind test from a classical density functional theory.

Jia Fu1, Yu Liu, Jianzhong Wu.   

Abstract

We report the performance of a classical density functional theory (CDFT) in the competition for the solvation free-energy category of the SAMPL4 blind prediction event. The theoretical calculations were carried out with the TIP3P water model and different combinations of solute configurations and molecular force fields. In comparison with the experimental data, the blind test yields an average unsigned error of 2.38 kcal/mol and the root mean square deviation of 2.99 kcal/mol. Whereas these numbers are significantly larger than the best results from explicit-solvent MD simulations, we find that the theoretical performance is sensitive to both the molecular force fields and solute configurations and that a comparable level of accuracy can be achieved by a judicious selection of the solute configurations and the force-field parameters. Most importantly, CDFT reduces the computational cost of MD simulation by almost 3 orders of magnitude, making it very attractive for large-scale hydration free-energy calculations (e.g., screening the aqueous solubility of drug-like molecules).

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Year:  2014        PMID: 24622881     DOI: 10.1007/s10822-014-9730-6

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  11 in total

1.  Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.

Authors:  Christopher J. Cramer; Donald G. Truhlar
Journal:  Chem Rev       Date:  1999-08-11       Impact factor: 60.622

2.  Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

Authors:  Araz Jakalian; David B Jack; Christopher I Bayly
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

3.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

4.  Continuous surface charge polarizable continuum models of solvation. I. General formalism.

Authors:  Giovanni Scalmani; Michael J Frisch
Journal:  J Chem Phys       Date:  2010-03-21       Impact factor: 3.488

5.  GROMACS: fast, flexible, and free.

Authors:  David Van Der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E Mark; Herman J C Berendsen
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

6.  Implicit solvent models.

Authors:  B Roux; T Simonson
Journal:  Biophys Chem       Date:  1999-04-05       Impact factor: 2.352

7.  Density-functional theory for complex fluids.

Authors:  Jianzhong Wu; Zhidong Li
Journal:  Annu Rev Phys Chem       Date:  2007       Impact factor: 12.703

8.  SAMPL4, a blind challenge for computational solvation free energies: the compounds considered.

Authors:  J Peter Guthrie
Journal:  J Comput Aided Mol Des       Date:  2014-04-06       Impact factor: 3.686

Review 9.  Blind prediction of solvation free energies from the SAMPL4 challenge.

Authors:  David L Mobley; Karisa L Wymer; Nathan M Lim; J Peter Guthrie
Journal:  J Comput Aided Mol Des       Date:  2014-03-11       Impact factor: 3.686

10.  A Site Density Functional Theory for Water: Application to Solvation of Amino Acid Side Chains.

Authors:  Yu Liu; Shuangliang Zhao; Jianzhong Wu
Journal:  J Chem Theory Comput       Date:  2013-03-28       Impact factor: 6.006

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  3 in total

1.  Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile.

Authors:  Caroline C Zanith; Josefredo R Pliego
Journal:  J Comput Aided Mol Des       Date:  2014-11-15       Impact factor: 3.686

2.  Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Authors:  Juyong Lee; Florentina Tofoleanu; Frank C Pickard; Gerhard König; Jing Huang; Ana Damjanović; Minkyung Baek; Chaok Seok; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

3.  Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.

Authors:  Luke J Gosink; Christopher C Overall; Sarah M Reehl; Paul D Whitney; David L Mobley; Nathan A Baker
Journal:  J Phys Chem B       Date:  2017-01-04       Impact factor: 2.991

  3 in total

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