Paper Info
Title
Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas.
Abstract
In the context of SAMPL5, we submitted blind predictions of the cyclohexane/water distribution coefficient (D) for a series of 53 drug-like molecules. Our method is purely empirical and based on the additive contribution of each solute atom to the free energy of solvation in water and in cyclohexane. The contribution of each atom depends on the atom type and on the exposed surface area. Comparatively to similar methods in the literature, we used a very small set of atomic parameters: only 10 for solvation in water and 1 for solvation in cyclohexane. As a result, the method is protected from overfitting and the error in the blind predictions could be reasonably estimated. Moreover, this approach is fast: it takes only 0.5 s to predict the distribution coefficient for all 53 SAMPL5 compounds, allowing its application in virtual screening campaigns. The performance of our approach (submission 49) is modest but satisfactory in view of its efficiency: the root mean square error (RMSE) was 3.3 log D units for the 53 compounds, while the RMSE of the best performing method (using COSMO-RS) was 2.1 (submission 16). Our method is implemented as a Python script available at .
Year
DOI
Venue
2016
https://doi.org/10.1007/s10822-016-9951-y
Journal of Computer-Aided Molecular Design
Keywords
Field
DocType
SAMPL5,Drug design data resource,D3R,Solvent accessible area,Free energy of solvation,Distribution coefficient
Cyclohexane,Computational chemistry,Chemistry,Mean squared error,Atom,Solvation,Overfitting,Partition coefficient,Small set
Journal
Volume
Issue
ISSN
30
11
0920-654X
Citations 
PageRank 
References 
0
0.34
0
Authors
3
Name
Order
Citations
PageRank
Diogo Santos-Martins192.89
Pedro Alexandrino Fernandes2477.17
Maria João Ramos3529.63