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Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F13%3A00074747" target="_blank" >RIV/00216224:14740/13:00074747 - isvavai.cz</a>

  • Result on the web

    <a href="http://pubs.acs.org/doi/pdf/10.1021/ci400448n" target="_blank" >http://pubs.acs.org/doi/pdf/10.1021/ci400448n</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1021/ci400448n" target="_blank" >10.1021/ci400448n</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

    Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

  • Original language description

    We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartre-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges welland were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

  • CEP classification

    CE - Biochemistry

  • OECD FORD branch

Result continuities

  • Project

    Result was created during the realization of more than one project. More information in the Projects tab.

  • Continuities

    P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Others

  • Publication year

    2013

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Name of the periodical

    Journal of Chemichal Information a Modeling

  • ISSN

    1549-9596

  • e-ISSN

  • Volume of the periodical

    53

  • Issue of the periodical within the volume

    10

  • Country of publishing house

    US - UNITED STATES

  • Number of pages

    11

  • Pages from-to

    2548-2558

  • UT code for WoS article

    000326480000007

  • EID of the result in the Scopus database