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@article{1317812,
author = {Geidl, Stanislav and Bouchal, Tomáš and Raček, Tomáš and Svobodová Vařeková, Radka and Hejret, Václav and Křenek, Aleš and Abagyan, Ruben and Koča, Jaroslav},
article_location = {London},
article_number = {DEC},
doi = {http://dx.doi.org/10.1186/s13321-015-0107-1},
keywords = {Partial atomic charges; Electronegativity Equalization Method; EEM; Quantum mechanics; QM; Drug-like molecules},
language = {eng},
issn = {1758-2946},
journal = {Journal of Cheminformatics},
title = {High-quality and universal empirical atomic charges for chemoinformatics applications},
url = {http://jcheminf.springeropen.com/articles/10.1186/s13321-015-0107-1},
volume = {7},
year = {2015}
}
TY - JOUR
ID - 1317812
AU - Geidl, Stanislav - Bouchal, Tomáš - Raček, Tomáš - Svobodová Vařeková, Radka - Hejret, Václav - Křenek, Aleš - Abagyan, Ruben - Koča, Jaroslav
PY - 2015
TI - High-quality and universal empirical atomic charges for chemoinformatics applications
JF - Journal of Cheminformatics
VL - 7
IS - DEC
SP - 1-10
EP - 1-10
PB - BIOMED CENTRAL LTD
SN - 17582946
KW - Partial atomic charges
KW - Electronegativity Equalization Method
KW - EEM
KW - Quantum mechanics
KW - QM
KW - Drug-like molecules
UR - http://jcheminf.springeropen.com/articles/10.1186/s13321-015-0107-1
L2 - http://jcheminf.springeropen.com/articles/10.1186/s13321-015-0107-1
N2 - Background: Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinformatics, as they are informative descriptors that can be utilised in pharmacophore design, virtual screening, similarity searches etc. Especially conformationally-dependent charges perform very successfully. In particular, their fast and accurate calculation via the Electronegativity Equalization Method (EEM) seems very promising for chemoinformatics applications. Unfortunately, published EEM parameter sets include only parameters for basic atom types and they often miss parameters for halogens, phosphorus, sulphur, triple bonded carbon etc. Therefore their applicability for drug-like molecules is limited. Results: We have prepared six EEM parameter sets which enable the user to calculate EEM charges in a quality comparable to quantum mechanics (QM) charges based on the most common charge calculation schemes (i.e., MPA, NPA and AIM) and a robust QM approach (HF/6-311G, B3LYP/6-311G). The calculated EEM parameters exhibited very good quality on a training set (R2 > 0.9) and also on a test set (R2 > 0.93). They are applicable for at least 95% of molecules in key drug databases (Drugbank, ChEMBL, Pubchem and ZINC) compared to less than 60% of the molecules from these databases for which currently used EEM parameters are applicable. Conclusions: We developed EEM parameters enabling the fast calculation of high-quality partial atomic charges for almost all drug-like molecules. In parallel, we provide a software solution for their easy computation. It enables the direct application of EEM in chemoinformatics.
ER -
GEIDL, Stanislav, Tomáš BOUCHAL, Tomáš RAČEK, Radka SVOBODOVÁ VAŘEKOVÁ, Václav HEJRET, Aleš KŘENEK, Ruben ABAGYAN and Jaroslav KOČA. High-quality and universal empirical atomic charges for chemoinformatics applications. \textit{Journal of Cheminformatics}. London: BIOMED CENTRAL LTD, 2015, vol.~7, DEC, p.~1-10. ISSN~1758-2946. Available from: https://dx.doi.org/10.1186/s13321-015-0107-1.
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