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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CE - Biochemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

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

Rok uplatnění

2013

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemichal Information a Modeling

ISSN

1549-9596

e-ISSN

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Svazek periodika

53

Číslo periodika v rámci svazku

10

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

11

Strana od-do

2548-2558

Kód UT WoS článku

000326480000007

EID výsledku v databázi Scopus

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