SQE charge calculation and its applicability for proteins

SCHINDLER, Ondřej, Tomáš RAČEK, Radka SVOBODOVÁ, Karel BERKA and Jaroslav KOČA. SQE charge calculation and its applicability for proteins. In ELIXIR CZ Annual Conference 2020. 2020. ISBN 978-80-86241-65-4.

Basic information

• Original name: SQE charge calculation and its applicability for proteins
• Authors: SCHINDLER, Ondřej (203 Czech Republic, belonging to the institution), Tomáš RAČEK (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ (203 Czech Republic, guarantor, belonging to the institution), Karel BERKA (203 Czech Republic, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, belonging to the institution).
• Edition: ELIXIR CZ Annual Conference 2020, 2020.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• RIV identification code: RIV/00216224:14740/20:00116809
• Organization unit: Central European Institute of Technology
• ISBN: 978-80-86241-65-4
• Keywords in English: partial atomic charges; empirical methods; SQE; proteins
• Tags: rivok

Abstract

Partial atomic charges are real numbers approximating a distribution of electron density among atoms of the molecule. They find applications in computational chemistry, chemoinformatics, bioinformatics and nanoscience. Because the charges are not physico- chemical observables but rather a theoretical concept, a lot of methods for their calculation were developed. The most reliable are quantum mechanical (QM) methods, but their strong disadvantage is the high computational complexity. Faster alternatives to QM methods are empirical charge calculation methods. They calculate charges based on common physico-chemical laws, but they include empirical parameters. Currently, frequently used empirical methods are EEM, QEq, and EQEq. However, even these advanced and popular methods have their limitations – e.g., their application for peptides, proteins, and other homogeneous molecular systems is problematic. A recent and promising empirical charge calculation method is a Split-charge Equilibration method (SQE). In this work, we introduce SQE extension SQE+qp, adapted for peptides. We also present an implementation of SQE and SQE+qp via a web application Atomic Charge Calculator II. Finally, we also present a method optGM for the fast parameterization of empirical charge calculation methods.

Links

• LQ1601, research and development project: Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR