SQE charge calculation and its applicability for proteins
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F20%3A00116809" target="_blank" >RIV/00216224:14740/20:00116809 - isvavai.cz</a>
Result on the web
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DOI - Digital Object Identifier
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Alternative languages
Result language
angličtina
Original language name
SQE charge calculation and its applicability for proteins
Original language description
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.
Czech name
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Czech description
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Classification
Type
O - Miscellaneous
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
<a href="/en/project/LQ1601" target="_blank" >LQ1601: CEITEC 2020</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů