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Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test

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Abstract

We report here a test of the Semi-Explicit Assembly (SEA) model in the solvation free energy category of the SAMPL3 blind prediction event (summer 2011). We tested how dependent the SEA results are on the chosen force field by performing calculations with both the General Amber and OPLS force fields. We compared our SEA results with full molecular dynamics simulations in explicit solvent. Of the 20 submissions, our SEA/OPLS results gave the second smallest RMS errors in free energies compared to experiments. SEA gives results that are very similar to those of its underlying force field and explicit solvent model. Hence, while the SEA water modeling approach is much faster than explicit solvent simulations, its predictions appear to be just as accurate.

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Acknowledgments

The authors thank Professor David Mobley for helpful discussions. The authors appreciate the support from NIH Grant GM063592.

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Authors and Affiliations

  1. Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, CA, 94158, USA

    Charles W. Kehoe

  2. Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA

    Christopher J. Fennell & Ken A. Dill

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  1. Charles W. Kehoe
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  2. Christopher J. Fennell
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  3. Ken A. Dill
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Correspondence to Ken A. Dill.

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Kehoe, C.W., Fennell, C.J. & Dill, K.A. Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. J Comput Aided Mol Des 26, 563–568 (2012). https://doi.org/10.1007/s10822-011-9536-8

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