Atomic Charge Calculator II: web-based tool for the calculation
of partial atomic charges

J 2020

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges

RAČEK, Tomáš, Ondřej SCHINDLER, Dominik TOUŠEK, Vladimír HORSKÝ, Karel BERKA et. al.

Základní údaje

Originální název

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges

Autoři

RAČEK, Tomáš (203 Česká republika, domácí), Ondřej SCHINDLER (203 Česká republika, domácí), Dominik TOUŠEK (203 Česká republika, domácí), Vladimír HORSKÝ (203 Česká republika, domácí), Karel BERKA (203 Česká republika), Jaroslav KOČA (203 Česká republika, domácí) a Radka SVOBODOVÁ (203 Česká republika, garant, domácí)

Vydání

Nucleic acids research, Oxford, Oxford University Press, 2020, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

domovská stránka výsledku

Impakt faktor

Impact factor: 16.971

Kód RIV

RIV/00216224:14740/20:00115952

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1093/nar/gkaa367

UT WoS

000562474100079

Klíčová slova anglicky

partial atomic charges; molecular structures; non-QM charge calculation methods; electrostatics; chemoinformatics

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 19. 1. 2021 16:04, Mgr. Marie Šípková, DiS.

Anotace

V originále

Partial atomic charges serve as a simple model for the electrostatic distribution of a molecule that drives its interactions with its surroundings. Since partial atomic charges are frequently used in computational chemistry, chemoinformatics and bioinformatics, many computational approaches for calculating them have been introduced. The most applicable are fast and reasonably accurate empirical charge calculation approaches. Here, we introduce Atomic Charge Calculator II (ACC II), a web application that enables the calculation of partial atomic charges via all the main empirical approaches and for all types of molecules. ACC II implements 17 empirical charge calculation methods, including the highly cited (QEq, EEM), the recently published (EQeq, EQeq+C), and the old but still often used (PEOE). ACC II enables the fast calculation of charges even for large macromolecular structures. The web server also offers charge visualization, courtesy of the powerful LiteMol viewer. The calculation setup of ACC II is very straightforward and enables the quick calculation of high-quality partial charges. The application is available at https://acc2.ncbr.muni.cz.

Návaznosti

EF16_013/0001777, projekt VaV

Název: ELIXIR-CZ: Budování kapacit

LM2018131, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

Přiložené soubory

gkaa367.pdf

Požádat o autorskou verzi souboru

Citovat

RAČEK, Tomáš, Ondřej SCHINDLER, Dominik TOUŠEK, Vladimír HORSKÝ, Karel BERKA, Jaroslav KOČA a Radka SVOBODOVÁ. Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic acids research. Oxford: Oxford University Press, 2020, roč. 48, W1, s. "W591"-"W596", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa367.

@article{1669836,
   author = {Raček, Tomáš and Schindler, Ondřej and Toušek, Dominik and Horský, Vladimír and Berka, Karel and Koča, Jaroslav and Svobodová, Radka},
   article_location = {Oxford},
   article_number = {W1},
   doi = {http://dx.doi.org/10.1093/nar/gkaa367},
   keywords = {partial atomic charges; molecular structures; non-QM charge calculation methods; electrostatics; chemoinformatics},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic acids research},
   title = {Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges},
   url = {https://doi.org/10.1093/nar/gkaa367},
   volume = {48},
   year = {2020}
}

TY  - JOUR
ID  - 1669836
AU  - Raček, Tomáš - Schindler, Ondřej - Toušek, Dominik - Horský, Vladimír - Berka, Karel - Koča, Jaroslav - Svobodová, Radka
PY  - 2020
TI  - Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges
JF  - Nucleic acids research
VL  - 48
IS  - W1
SP  - "W591"-"W596"
EP  - "W591"-"W596"
PB  - Oxford University Press
SN  - 03051048
KW  - partial atomic charges
KW  - molecular structures
KW  - non-QM charge calculation methods
KW  - electrostatics
KW  - chemoinformatics
UR  - https://doi.org/10.1093/nar/gkaa367
L2  - https://doi.org/10.1093/nar/gkaa367
N2  - Partial atomic charges serve as a simple model for the electrostatic distribution of a molecule that drives its interactions with its surroundings. Since partial atomic charges are frequently used in computational chemistry, chemoinformatics and bioinformatics, many computational approaches for calculating them have been introduced. The most applicable are fast and reasonably accurate empirical charge calculation approaches. Here, we introduce Atomic Charge Calculator II (ACC II), a web application that enables the calculation of partial atomic charges via all the main empirical approaches and for all types of molecules. ACC II implements 17 empirical charge calculation methods, including the highly cited (QEq, EEM), the recently published (EQeq, EQeq+C), and the old but still often used (PEOE). ACC II enables the fast calculation of charges even for large macromolecular structures. The web server also offers charge visualization, courtesy of the powerful LiteMol viewer. The calculation setup of ACC II is very straightforward and enables the quick calculation of high-quality partial charges. The application is available at https://acc2.ncbr.muni.cz.
ER  -

RAČEK, Tomáš, Ondřej SCHINDLER, Dominik TOUŠEK, Vladimír HORSKÝ, Karel BERKA, Jaroslav KOČA a Radka SVOBODOVÁ. Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2020, roč.~48, W1, s.~''W591''-''W596'', 6 s. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa367.

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