AtomicChargeCalculator: Interactive Web-based calculation of atomic charges in large biomolecular complexes and drug like molecules

IONESCU, Crina-Maria, David SEHNAL, Francesco Luca FALGINELLA, Purbaj PANT, Lukáš PRAVDA, Tomáš BOUCHAL, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL and Jaroslav KOČA. AtomicChargeCalculator: Interactive Web-based calculation of atomic charges in large biomolecular complexes and drug like molecules. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2015, vol. 7, No 50, p. "nestránkováno", 13 pp. ISSN 1758-2946. doi:10.1186/s13321-015-0099-x.

Basic information

• Original name: AtomicChargeCalculator: Interactive Web-based calculation of atomic charges in large biomolecular complexes and drug like molecules
• Authors: IONESCU, Crina-Maria (642 Romania, belonging to the institution), David SEHNAL (203 Czech Republic, belonging to the institution), Francesco Luca FALGINELLA (380 Italy, belonging to the institution), Purbaj PANT (524 Nepal, belonging to the institution), Lukáš PRAVDA (203 Czech Republic, belonging to the institution), Tomáš BOUCHAL (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution), Stanislav GEIDL (203 Czech Republic, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution).
• Edition: Journal of Cheminformatics, London, BIOMED CENTRAL LTD, 2015, 1758-2946.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 3.949
• RIV identification code: RIV/00216224:14310/15:00081192
• Organization unit: Faculty of Science
• Doi: http://dx.doi.org/10.1186/s13321-015-0099-x
• UT WoS: 000363291500001
• Keywords in English: Conformationally dependent atomic charges; Biomacromolecules; Drug-like molecules; Paracetamol; Benzoic acids; Protegrin; Proteasome; Allostery; Chemical reactivity
• Tags: AKR, rivok
• Tags: International impact, Reviewed

Abstract

This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form.

Links

• ED1.1.00/02.0068, research and development project: Name: CEITEC - central european institute of technology
• EE2.3.30.0009, research and development project: Name: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci
• GA13-25401S, research and development project: Name: Studium proteinů z patogenů zapojených do rozpoznávání hostitelského organismu

Investor: Czech Science Foundation

• MUNI/A/1159/2014, interní kód MU: Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IV.

Investor: Masaryk University, Category A