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J Comput Aided Mol Des. 2016 Nov;30(11):1129-1138. doi: 10.1007/s10822-016-9964-6. Epub 2016 Sep 19.

Partition coefficients for the SAMPL5 challenge using transfer free energies.

Author information

1
Department of Chemistry, Michigan State University, 578 S. Shaw Ln, East Lansing, MI, 48824, USA.
2
Laboratory of Computational Biology, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA.
3
Department of Chemistry, Michigan State University, 578 S. Shaw Ln, East Lansing, MI, 48824, USA. wilson@chemistry.msu.edu.

Abstract

SAMPL challenges (Mobley et al. in J Comput Aided Mol Des 28:135-150, 2014; Skillman in J Comput Aided Mol Des 26:473-474, 2012; Geballe in J Comput Aided Mol Des 24:259-279, 2010; Guthrie in J Phys Chem B 113:4501-4507, 2009) provide excellent opportunities to assess theoretical approaches on new data sets with a goal of gaining greater insight towards protein and ligand modeling. In the SAMPL5 experiment, cyclohexane-water partition coefficients were determined using a vertical solvation scheme in conjunction with the SMD continuum solvent model. Several DFT functionals partnered with correlation consistent basis sets were evaluated for the prediction of the partition coefficients. The approach chosen for the competition, a B3PW91 vertical solvation scheme, yields a mean absolute deviation of 1.9 logP units and performs well at estimating the correct hydrophilicity and hydrophobicity for the full SAMPL5 molecule set.

KEYWORDS:

B3PW91; Cyclohexane; DFT; Distribution coefficient; Partition coefficient; SAMPL; SMD; Solvation; Water

PMID:
27646287
PMCID:
PMC6561331
DOI:
10.1007/s10822-016-9964-6
[Indexed for MEDLINE]
Free PMC Article

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