How well do semiempirical QM methods describe the structure of proteins?

Kód výsledku v IS VaVaI

RIV/61388963:_____/23:00568443 - isvavai.cz

Výsledek na webu

https://doi.org/10.1063/5.0135091

DOI - Digital Object Identifier

10.1063/5.0135091

Jazyk výsledku

angličtina

Název v původním jazyce

How well do semiempirical QM methods describe the structure of proteins?

Popis výsledku v původním jazyce

Semiempirical quantum-mechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: The ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6-D3H4, PM7, and GFN2-xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6-D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.

Název v anglickém jazyce

How well do semiempirical QM methods describe the structure of proteins?

Popis výsledku anglicky

Semiempirical quantum-mechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: The ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6-D3H4, PM7, and GFN2-xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6-D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

GA22-17063S: Nová generace semiempirických kvantově-mechanických metod založená na velkých datech

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Physics

ISSN

0021-9606

e-ISSN

1089-7690

Svazek periodika

158

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

8

Strana od-do

044118

Kód UT WoS článku

000922928600001

EID výsledku v databázi Scopus

2-s2.0-85147090256