How well do semiempirical QM methods describe the structure of proteins?
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F23%3A00568443" target="_blank" >RIV/61388963:_____/23:00568443 - isvavai.cz</a>
Result on the web
<a href="https://doi.org/10.1063/5.0135091" target="_blank" >https://doi.org/10.1063/5.0135091</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1063/5.0135091" target="_blank" >10.1063/5.0135091</a>
Alternative languages
Result language
angličtina
Original language name
How well do semiempirical QM methods describe the structure of proteins?
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
<a href="/en/project/GA22-17063S" target="_blank" >GA22-17063S: Data-driven approach to the development of next-generation semiempirical QM methods</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2023
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 Chemical Physics
ISSN
0021-9606
e-ISSN
1089-7690
Volume of the periodical
158
Issue of the periodical within the volume
4
Country of publishing house
US - UNITED STATES
Number of pages
8
Pages from-to
044118
UT code for WoS article
000922928600001
EID of the result in the Scopus database
2-s2.0-85147090256