Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F15%3A10315393" target="_blank" >RIV/00216208:11310/15:10315393 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/61388963:_____/15:00449320 RIV/61989592:15310/15:33157045

Výsledek na webu

<a href="http://dx.doi.org/10.1021/acs.jctc.5b00398" target="_blank" >http://dx.doi.org/10.1021/acs.jctc.5b00398</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.5b00398" target="_blank" >10.1021/acs.jctc.5b00398</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

Popis výsledku v původním jazyce

Representative pairs of amino acid side chains and nucleic acid bases extracted from available high-quality structures of protein DNA complexes were analyzed using a range of computational methods. CCSD(T)/CBS interaction energies were calculated for thechosen 272 pairs. These reference interaction energies were used to test the MP2.5/CBS, MP2.X/ CBS, MP2-F12, DFT-D3, PM6, and Amber force field methods. Method MP2.5 provided excellent agreement with reference data (root-mean-square error (RMSE) of 0.11kcal/mol), which is more than 1 order of magnitude faster than the CCSD(T) method. When MP2-F12 and MP2.5 were combined, the results were within reasonable accuracy (0.20 kcal/mol), with a computational savings of almost 2 orders of magnitude: Therefore, this method is a promising tool for accurate calculations of interaction energies in protein DNA motifs of up to similar to 100 atoms, for which CCSD(T)/CBS benchmark calculations are not feasible. B3-LYP-D3 calculated with def2-TZVPP a

Název v anglickém jazyce

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

Popis výsledku anglicky

Representative pairs of amino acid side chains and nucleic acid bases extracted from available high-quality structures of protein DNA complexes were analyzed using a range of computational methods. CCSD(T)/CBS interaction energies were calculated for thechosen 272 pairs. These reference interaction energies were used to test the MP2.5/CBS, MP2.X/ CBS, MP2-F12, DFT-D3, PM6, and Amber force field methods. Method MP2.5 provided excellent agreement with reference data (root-mean-square error (RMSE) of 0.11kcal/mol), which is more than 1 order of magnitude faster than the CCSD(T) method. When MP2-F12 and MP2.5 were combined, the results were within reasonable accuracy (0.20 kcal/mol), with a computational savings of almost 2 orders of magnitude: Therefore, this method is a promising tool for accurate calculations of interaction energies in protein DNA motifs of up to similar to 100 atoms, for which CCSD(T)/CBS benchmark calculations are not feasible. B3-LYP-D3 calculated with def2-TZVPP a

Druh

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

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

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

Návaznosti

S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2015

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Svazek periodika

11

Číslo periodika v rámci svazku

9

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

7

Strana od-do

4086-4092

Kód UT WoS článku

000361087600013

EID výsledku v databázi Scopus

2-s2.0-84941129427