SQE charge calculation and its applicability for proteins

a 2020

SQE charge calculation and its applicability for proteins

SCHINDLER, Ondřej, Tomáš RAČEK, Radka SVOBODOVÁ, Karel BERKA, Jaroslav KOČA et. al.

Základní údaje

Originální název

SQE charge calculation and its applicability for proteins

Autoři

SCHINDLER, Ondřej (203 Česká republika, domácí), Tomáš RAČEK (203 Česká republika, domácí), Radka SVOBODOVÁ (203 Česká republika, garant, domácí), Karel BERKA (203 Česká republika, domácí) a Jaroslav KOČA (203 Česká republika, domácí)

Vydání

ELIXIR CZ Annual Conference 2020, 2020

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

Kód RIV

RIV/00216224:14740/20:00116809

Organizační jednotka

Středoevropský technologický institut

ISBN

978-80-86241-65-4

Klíčová slova anglicky

partial atomic charges; empirical methods; SQE; proteins

Štítky

rivok

Změněno: 18. 3. 2021 20:16, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

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.

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

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

@proceedings{1688880,
   author = {Schindler, Ondřej and Raček, Tomáš and Svobodová, Radka and Berka, Karel and Koča, Jaroslav},
   booktitle = {ELIXIR CZ Annual Conference 2020},
   keywords = {partial atomic charges; empirical methods; SQE; proteins},
   language = {eng},
   isbn = {978-80-86241-65-4},
   title = {SQE charge calculation and its applicability for proteins},
   year = {2020}
}

TY  - CONF
ID  - 1688880
AU  - Schindler, Ondřej - Raček, Tomáš - Svobodová, Radka - Berka, Karel - Koča, Jaroslav
PY  - 2020
TI  - SQE charge calculation and its applicability for proteins
SN  - 9788086241654
KW  - partial atomic charges
KW  - empirical methods
KW  - SQE
KW  - proteins
N2  - 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.
ER  -

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

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