SQE charge calculation and its applicability for proteins

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.

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

• Originální 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

Anotace

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