Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes
dc.contributor.author | Knight, Jennifer L. | en_US |
dc.contributor.author | Yesselman, Joseph D. | en_US |
dc.contributor.author | Brooks, Charles L. | en_US |
dc.date.accessioned | 2013-04-08T20:50:10Z | |
dc.date.available | 2014-05-23T15:04:20Z | en_US |
dc.date.issued | 2013-04-30 | en_US |
dc.identifier.citation | Knight, Jennifer L.; Yesselman, Joseph D.; Brooks, Charles L. (2013). "Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes." Journal of Computational Chemistry 34(11): 893-903. <http://hdl.handle.net/2027.42/97284> | en_US |
dc.identifier.issn | 0192-8651 | en_US |
dc.identifier.issn | 1096-987X | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/97284 | |
dc.description.abstract | Multipurpose atom‐typer for CHARMM (MATCH), an atom‐typing toolset for molecular mechanics force fields, was recently developed in our laboratory. Here, we assess the ability of MATCH‐generated parameters and partial atomic charges to reproduce experimental absolute hydration free energies for a series of 457 small neutral molecules in GBMV2, Generalized Born with a smooth SWitching (GBSW), and fast analytical continuum treatment of solvation (FACTS) implicit solvent models. The quality of hydration free energies associated with small molecule parameters obtained from ParamChem, SwissParam, and Antechamber are compared. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, these automated parameterization schemes with GBMV2 and GBSW demonstrate reasonable agreement with experimental hydration free energies (average unsigned errors of 0.9–1.5 kcal/mol and R 2 of 0.63–0.87). GBMV2 and GBSW consistently provide slightly more accurate estimates than FACTS, whereas Antechamber parameters yield marginally more accurate estimates than the current generation of MATCH, ParamChem, and SwissParam parameterization strategies. Modeling with MATCH libraries that are derived from different CHARMM topology and parameter files highlights the importance of having sufficient coverage of chemical space within the underlying databases of these automated schemes and the benefit of targeting specific functional groups for parameterization efforts to maximize both the breadth and the depth of the parameterized space. © 2013 Wiley Periodicals, Inc. Ligand parameterization for molecular mechanics simulations is computationally intensive, requiring long multistep optimization procedures. Recently there has been an influx of automated parameterization tools for the CHARMM force field. These tools radically speed up the process, but it remains unclear whether accuracy is sacrificed to a significant extent. The research presented in this article uses a set of 457 small molecules to quantify the accuracy of four automated parameterization tools by computing absolute hydration free energies. | en_US |
dc.publisher | Wiley Subscription Services, Inc., A Wiley Company | en_US |
dc.subject.other | Implicit Solvent Models | en_US |
dc.subject.other | CHARMM | en_US |
dc.subject.other | Hydration Free Energies | en_US |
dc.subject.other | Ligand Parameterization | en_US |
dc.title | Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Chemical Engineering | en_US |
dc.subject.hlbsecondlevel | Chemistry | en_US |
dc.subject.hlbsecondlevel | Materials Science and Engineering | en_US |
dc.subject.hlbtoplevel | Engineering | en_US |
dc.subject.hlbtoplevel | Science | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Department of Chemistry University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109 | en_US |
dc.contributor.affiliationum | Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109 | en_US |
dc.contributor.affiliationum | Department of Chemistry University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109 | en_US |
dc.identifier.pmid | 23292859 | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/97284/1/23199_ftp.pdf | |
dc.identifier.doi | 10.1002/jcc.23199 | en_US |
dc.identifier.source | Journal of Computational Chemistry | en_US |
dc.identifier.citedreference | N. Haider, Molecules 2010, 15, 5079. | en_US |
dc.identifier.citedreference | J. Wang, R. Wolf, J. Caldwell, P. Kollman, D. Case, J. Comput. Chem. 2004, 25, 1157. | en_US |
dc.identifier.citedreference | D. L. Mobley, K. A. Dill, J. D. Chodera, J. Phys. Chem. B 2008, 112, 938. | en_US |
dc.identifier.citedreference | D. L. Mobley, C. I. Bayly, M. D. Cooper, M. R. Shirts, K. A. Dill, J. Chem. Theory Comput. 2009, 5, 350. | en_US |
dc.identifier.citedreference | D. Shivakumar, Y. Deng, B. Roux, J. Chem. Theory Comput. 2009, 5, 919. | en_US |
dc.identifier.citedreference | D. Shivakumar, J. Williams, Y. Wu, W. Damm, J. Shelley, W. Sherman, J. Chem. Theory Comput. 2010, 6, 1509. | en_US |
dc.identifier.citedreference | J. L. Knight, C. L. Brooks, III, J. Comput. Chem. 2011, 32, 2909. | en_US |
dc.identifier.citedreference | W. C. Still, A. Tempczyk, R. C. Hawley, T. Hendrickson, J. Am. Chem. Soc. 1990, 112, 6127. | en_US |
dc.identifier.citedreference | M. Feig, C. L. Brooks, III, Curr. Opin. Struct. Biol. 2004, 14, 217. | en_US |
dc.identifier.citedreference | M. Born, Z. Phys. 1920, 1, 45. | en_US |
dc.identifier.citedreference | M. Lee, M. Feig, F. Salsbury, C. L. Brooks, III, J. Comput. Chem. 2003, 24, 1348. | en_US |
dc.identifier.citedreference | M. S. Lee, F. Salsbury, C. L. Brooks, III, J. Chem. Phys. 2002, 116, 10606. | en_US |
dc.identifier.citedreference | W. Im, M. Lee, C. L. Brooks, III, J. Comput. Chem. 2003, 24, 1691. | en_US |
dc.identifier.citedreference | U. Haberthuer, A. Caflisch, J. Comput. Chem. 2008, 29, 701. | en_US |
dc.identifier.citedreference | U. Haberthur, N. Majeux, P. Werner, A. Caflisch, J. Comput. Chem. 2003, 24, 1936. | en_US |
dc.identifier.citedreference | R. Rizzo, T. Aynechi, D. Case, I. Kuntz, J. Chem. Theory Comput. 2006, 2, 128. | en_US |
dc.identifier.citedreference | J. P. Guthrie, J. Phys. Chem. B 2009, 113, 4501. | en_US |
dc.identifier.citedreference | D. Mobley, E. Dumont, J. Chodera, K. Dill, J. Phys. Chem. B 2007, 111, 2242. | en_US |
dc.identifier.citedreference | A. Nicholls, D. L. Mobley, J. P. Guthrie, J. D. Chodera, C. I. Bayly, M. D. Cooper, V. S. Pande, J. Med. Chem. 2008, 51, 769. | en_US |
dc.identifier.citedreference | A. Jakalian, B. Bush, D. Jack, C. Bayly, J. Comput. Chem. 2000, 21, 132. | en_US |
dc.identifier.citedreference | A. Jakalian, D. Jack, C. Bayly, J. Comput. Chem. 2002, 23, 1623. | en_US |
dc.identifier.citedreference | W. F. van Gunsteren, H. J. C. Berendsen, Mol. Phys. 1977, 34, 1311. | en_US |
dc.identifier.citedreference | B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus. J. Comput. Chem. 1983, 4, 187. | en_US |
dc.identifier.citedreference | B. R. Brooks, C. L. Brooks, III, A. D. Mackerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, J. Comput. Chem. 2009, 30, 1545. | en_US |
dc.identifier.citedreference | C. H. Bennett, J. Comput. Phys. 1976, 22, 245. | en_US |
dc.identifier.citedreference | M. R. Shirts, J. D. Chodera, J. Chem. Phys. 2008, 129, 124105. | en_US |
dc.identifier.citedreference | T. A. Halgren, J. Comput. Chem. 1998, 17, 520. | en_US |
dc.identifier.citedreference | J. D. Yesselman, D. J. Price, J. L. Knight, L. C. Brooks, III, J. Comput. Chem. 2011, 33, 189. | en_US |
dc.identifier.citedreference | K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A. D. Mackerell, Jr., J. Comput. Chem. 2010, 31, 671. | en_US |
dc.identifier.citedreference | T. A. Halgren, J. Comput. Chem. 1999, 20, 730. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.