Fast estimation of solvation free energies for diverse chemical species

The Journal of Physical Chemistry. B
Robert D Boyer, Richard L Bryan

Abstract

The free energy of solvation can play an important or even dominant role in the accurate prediction of binding affinities and various other molecular-scale interaction phenomena critical to the study of biochemical processes. Many research applications for solvation modeling, such as fragment-based drug design, require algorithms that are both accurate and computationally inexpensive. We have developed a calculation of solvation free energy which runs fast enough for interactive applications, functions for a wide range of chemical species relevant to simulating molecules for biological and pharmaceutical applications, and is readily extended when data for new species becomes available. We have also demonstrated that the incorporation of ab initio data provides necessary access to sufficient reference data for a broad range of chemical features. Our empirical model, including an electrostatic term and a different set of atom types, demonstrates improvements over a previous, solvent-accessible surface area-only model by Wang et al. when fit to identical training sets (mean absolute error of 0.513 kcal/mol versus the 0.538 kcal/mol reported by Wang). The incorporation of ab initio solvation free energies provides a significant inc...Continue Reading

References

Jan 1, 1990·Annual Review of Biophysics and Biophysical Chemistry·K A Sharp, B Honig
May 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·T OoiH A Scheraga
Sep 15, 1973·Journal of Molecular Biology·A Shrake, J A Rupley
Feb 14, 1971·Journal of Molecular Biology·B Lee, F M Richards
Sep 1, 1999·Proceedings of the National Academy of Sciences of the United States of America·I D KuntzP A Kollman
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Apr 26, 2005·The Journal of Chemical Physics·Michael R Shirts, Vijay S Pande
Oct 4, 2005·Journal of Computational Chemistry·David A CaseRobert J Woods
Feb 7, 2006·Journal of Molecular Graphics & Modelling·Junmei WangDavid A Case
Jan 4, 2008·The Journal of Physical Chemistry. B·David L MobleyJohn D Chodera
Jan 25, 2008·Journal of Medicinal Chemistry·Anthony NichollsVijay S Pande
Jun 3, 2008·Accounts of Chemical Research·Christopher J Cramer, Donald G Truhlar
Oct 30, 2008·The Journal of Physical Chemistry. B·Pei-Kun Yang, Carmay Lim
Jan 24, 2009·Current Opinion in Structural Biology·Olgun Guvench, Alexander D MacKerell
Mar 14, 2009·The Journal of Physical Chemistry. B·Anthony NichollsJ Andrew Grant
Apr 3, 2009·The Journal of Physical Chemistry. B·J Peter Guthrie
Feb 13, 2010·Journal of Chemical Theory and Computation·David L MobleyKen A Dill
Dec 8, 2010·Journal of Chemical Information and Modeling·Sehan LeeKyoung Tai No
Jul 7, 2011·Journal of the American Chemical Society·Samuel GenhedenUlf Ryde
Jul 8, 2011·Journal of Computational Chemistry·Jennifer L Knight, Charles L Brooks
Jul 28, 2011·Journal of the American Chemical Society·Jasmin MecinovićGeorge M Whitesides
Feb 1, 2012·Journal of Computer-aided Molecular Design·John L KulpFrank Guarnieri
Apr 14, 2009·Journal of Chemical Theory and Computation·Devleena ShivakumarBenoît Roux
May 11, 2010·Journal of Chemical Theory and Computation·Devleena ShivakumarWoody Sherman

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Citations

Feb 21, 2014·Journal of Computer-aided Molecular Design·Hwangseo Park
Jul 20, 2013·The Journal of Physical Chemistry. B·Satoshi TakayasuKazuteru Shinozaki
Sep 3, 2016·Journal of Computer-aided Molecular Design·Diogo Santos-MartinsMaria João Ramos
Jun 11, 2013·Journal of Chemical Theory and Computation·Alauddin Ahmed, Stanley I Sandler

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