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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

  • DOI - Digital Object Identifier

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

  • Czech description

Classification

  • Type

    O - Miscellaneous

  • CEP classification

  • 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