All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5
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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Genheden, Samuel
cc461200-48bd-411b-8424-23dfef65cc86
Essex, Jonathan
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Genheden, Samuel
cc461200-48bd-411b-8424-23dfef65cc86
Essex, Jonathan
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Genheden, Samuel and Essex, Jonathan
(2016)
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.
Journal of Computer-Aided Molecular Design, .
(doi:10.1007/s10822-016-9926-z).
Abstract
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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Accepted/In Press date: 16 July 2016
e-pub ahead of print date: 26 July 2016
Organisations:
Computational Systems Chemistry
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Local EPrints ID: 402206
URI: http://eprints.soton.ac.uk/id/eprint/402206
ISSN: 0920-654X
PURE UUID: d9cc75e0-2262-498c-a950-7d1e332a059a
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Date deposited: 03 Nov 2016 15:04
Last modified: 16 Mar 2024 02:45
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Author:
Samuel Genheden
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