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
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CE - Biochemistry
OECD FORD branch
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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
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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
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