High-quality and universal empirical atomic charges for
chemoinformatics applications

J 2015

High-quality and universal empirical atomic charges for chemoinformatics applications

GEIDL, Stanislav, Tomáš BOUCHAL, Tomáš RAČEK, Radka SVOBODOVÁ VAŘEKOVÁ, Václav HEJRET et. al.

Základní údaje

Originální název

High-quality and universal empirical atomic charges for chemoinformatics applications

Autoři

GEIDL, Stanislav (203 Česká republika, domácí), Tomáš BOUCHAL (203 Česká republika, domácí), Tomáš RAČEK (203 Česká republika, domácí), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, domácí), Václav HEJRET (203 Česká republika, domácí), Aleš KŘENEK (203 Česká republika, domácí), Ruben ABAGYAN (840 Spojené státy) a Jaroslav KOČA (203 Česká republika, garant, domácí)

Vydání

Journal of Cheminformatics, London, BIOMED CENTRAL LTD, 2015, 1758-2946

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.949

Kód RIV

RIV/00216224:14740/15:00081211

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1186/s13321-015-0107-1

UT WoS

000366278000001

Klíčová slova anglicky

Partial atomic charges; Electronegativity Equalization Method; EEM; Quantum mechanics; QM; Drug-like molecules

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 29. 3. 2016 11:06, Olga Křížová

Anotace

V originále

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.20.0042, projekt VaV

Název: Internacionalizace programu Strukturní biologie s důrazem na rozvoj nových směrů výzkumu

EE2.3.30.0009, projekt VaV

Název: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GA13-25401S, projekt VaV

Název: Studium proteinů z patogenů zapojených do rozpoznávání hostitelského organismu

Investor: Grantová agentura ČR, Studium proteinu z patogenu zapojených do rozpoznávání hostitelského organismu

MUNI/A/1159/2014, interní kód MU

Název: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IV.

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IV., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

GEIDL, Stanislav, Tomáš BOUCHAL, Tomáš RAČEK, Radka SVOBODOVÁ VAŘEKOVÁ, Václav HEJRET, Aleš KŘENEK, Ruben ABAGYAN a Jaroslav KOČA. High-quality and universal empirical atomic charges for chemoinformatics applications. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2015, roč. 7, DEC, s. 1-10. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-015-0107-1.

@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 a Jaroslav KOČA. High-quality and universal empirical atomic charges for chemoinformatics applications. \textit{Journal of Cheminformatics}. London: BIOMED CENTRAL LTD, 2015, roč.~7, DEC, s.~1-10. ISSN~1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-015-0107-1.

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