QM-like partial atomic charges for proteins available online

a 2021

QM-like partial atomic charges for proteins available online

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

Základní údaje

Originální název

QM-like partial atomic charges for proteins available online

Autoři

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

Vydání

ELIXIR CZ Annual Conference 2021, 2021

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Organizační jednotka

Středoevropský technologický institut

ISBN

978-80-86241-67-8

Klíčová slova česky

Parciální atomové náboje, proteiny, SQE+qp

Změněno: 19. 4. 2022 12:11, RNDr. Ondřej Schindler, Ph.D.

Anotace

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.

Citovat

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

@proceedings{1847019,
   author = {Schindler, Ondřej and Raček, Tomáš and Svobodová, Radka and Berka, Karel},
   booktitle = {ELIXIR CZ Annual Conference 2021},
   language = {eng},
   isbn = {978-80-86241-67-8},
   title = {QM-like partial atomic charges for proteins available online},
   year = {2021}
}

TY  - CONF
ID  - 1847019
AU  - Schindler, Ondřej - Raček, Tomáš - Svobodová, Radka - Berka, Karel
PY  - 2021
TI  - QM-like partial atomic charges for proteins available online
SN  - 9788086241678
N2  - 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.
ER  -

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

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