QM-like partial atomic charges for proteins available online

SCHINDLER, Ondřej, Tomáš RAČEK, Radka SVOBODOVÁ and Karel BERKA. QM-like partial atomic charges for proteins available online. In ELIXIR CZ Annual Conference 2021. 2021. ISBN 978-80-86241-67-8.

Basic information

Original name

QM-like partial atomic charges for proteins available online

Authors

SCHINDLER, Ondřej, Tomáš RAČEK, Radka SVOBODOVÁ and Karel BERKA

Edition

ELIXIR CZ Annual Conference 2021, 2021

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Other information

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Organization unit

Central European Institute of Technology

ISBN

978-80-86241-67-8

Keywords (in Czech)

Parciální atomové náboje, proteiny, SQE+qp

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Abstract

V originále

PARTIAL ATOMIC CHARGES are real numbers assigned to individual atoms of a molecule that approximate the distribution of electron density among these atoms. Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. In general, there are two approaches to calculate partial atomic charges. The partial atomic charges approximate the electron density and therefore the most reliable way is to obtain them directly from the electron density by some quantum mechanical method (QM). A substantial disadvantage of QM approaches is their high computational complexity, and therefore a long computational time. For this reason, QM methods are inapplicable for proteins. EMPIRICAL CHARGE CALCULATION METHODS are faster alternatives to QM methods. Empirical methods use only the positions of atoms, some of their characteristics (e.g. electronegativity, chemical hardness, etc.) and possibly the bonds between them to calculate partial atomic charges. Many empirical methods have already been developed. However, these methods have their limitations—e.g., their application for proteins and other homogeneous macromolecular systems composed from just several types of residues is problematic. SPLIT-CHARGE EQUILIBRATION WITH PARAMETERIZED INITIAL CHARGES (SQE+qp) [1] adapted proteins is introduced in this work. Our method can reproduce QM partial atomic charges with high accuracy. We also present an implementation of SQE+qp via a web application Atomic Charge Calculator II (ACC II) [2]. We provide the scientific community a freely available online tool for the calculation of QM-like partial atomic charges. [1] Schindler, O., Raček, T., Maršavelski, A., Koča, J., Berka, K. and Svobodová, R., 2021. Optimized SQE atomic charges for peptides accessible via a web application. Journal of cheminformatics, 13(1), pp.1-11. [2] Raček, T., Schindler, O., Toušek, D., Horský, V., Berka, K., Koča, J. and Svobodová, R., 2020. Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic acids research, 48(W1), pp.W591-W596.