Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Issue Volume 48:Issue W1(2020) (13th May 2020)

• Record Type: Journal Article
• Authors: Raček, Tomáš; Schindler, Ondřej; Toušek, Dominik; Horský, Vladimír; Berka, Karel; Koča, Jaroslav; Svobodová, Radka
• Is Part Of: Nucleic acids research. Volume 48:Issue W1(2020)
• Page Start: W591
• Page End: W596
• Publication Date: 2020-05-13
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa367
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: 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 .