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Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges
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 calc...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319571/ https://www.ncbi.nlm.nih.gov/pubmed/32402071 http://dx.doi.org/10.1093/nar/gkaa367 |
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author | Raček, Tomáš Schindler, Ondřej Toušek, Dominik Horský, Vladimír Berka, Karel Koča, Jaroslav Svobodová, Radka |
author_facet | Raček, Tomáš Schindler, Ondřej Toušek, Dominik Horský, Vladimír Berka, Karel Koča, Jaroslav Svobodová, Radka |
author_sort | Raček, Tomáš |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7319571 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-73195712020-07-01 Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges Raček, Tomáš Schindler, Ondřej Toušek, Dominik Horský, Vladimír Berka, Karel Koča, Jaroslav Svobodová, Radka Nucleic Acids Res Web Server Issue 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. Oxford University Press 2020-07-02 2020-05-13 /pmc/articles/PMC7319571/ /pubmed/32402071 http://dx.doi.org/10.1093/nar/gkaa367 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue Raček, Tomáš Schindler, Ondřej Toušek, Dominik Horský, Vladimír Berka, Karel Koča, Jaroslav Svobodová, Radka Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges |
title | Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges |
title_full | Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges |
title_fullStr | Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges |
title_full_unstemmed | Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges |
title_short | Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges |
title_sort | atomic charge calculator ii: web-based tool for the calculation of partial atomic charges |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319571/ https://www.ncbi.nlm.nih.gov/pubmed/32402071 http://dx.doi.org/10.1093/nar/gkaa367 |
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