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Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.

ABSTRACT: Several submissions for the SAMPL4 hydration free energy set were calculated using OpenEye tools, including many that were among the top performing submissions. All of our best submissions used AM1BCC charges and Poisson-Boltzmann solvation. Three submissions used a single conformer for calculating the hydration free energy and all performed very well with mean unsigned errors ranging from 0.94 to 1.08 kcal/mol. These calculations were very fast, only requiring 0.5-2.0 s per molecule. We observed that our two single-conformer methodologies have different types of failure cases and that these differences could be exploited for determining when the methods are likely to have substantial errors.

SUBMITTER: Ellingson BA

PROVIDER: S-EPMC4003403 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.

Ellingson Benjamin A BA Geballe Matthew T MT Wlodek Stanislaw S Bayly Christopher I CI Skillman A Geoffrey AG Nicholls Anthony A

Journal of computer-aided molecular design 20140316 3

Several submissions for the SAMPL4 hydration free energy set were calculated using OpenEye tools, including many that were among the top performing submissions. All of our best submissions used AM1BCC charges and Poisson-Boltzmann solvation. Three submissions used a single conformer for calculating the hydration free energy and all performed very well with mean unsigned errors ranging from 0.94 to 1.08 kcal/mol. These calculations were very fast, only requiring 0.5-2.0 s per molecule. We observe ...[more]

PMID: 24633516

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