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All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5

Journal article
Authors Samuel Genheden
Jonathan W. Essex
Published in Journal of Computer-Aided Molecular Design
Volume 30
Issue 11
Pages 969-976
ISSN 0920-654X
Publication year 2016
Published at Department of Chemistry and Molecular Biology
Pages 969-976
Language en
Keywords Distribution coefficients, Multiscaling, Hybrid model, AA/CG, Elba, SAMPL5
Subject categories Theoretical Chemistry


We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent.

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