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Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures

SYSNO ASEP	0324799
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures
Title	Reprezentativní interakce aminokyselin v proteinech: srovnání přesných ab-initio kvantově chemických výpočtů s empirickými potenciály
Author(s)	Berka, Karel (UOCHB-X) Laskowski, R. (GB) Riley, K. E. (PR) Hobza, Pavel (UOCHB-X)_{RID, ORCID} Vondrášek, Jiří (UOCHB-X)_{RID, ORCID}
Number of authors	5
Source Title	Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618 Roč. 5, č. 4 (2009), s. 982-992
Number of pages	11 s.
Language	eng - English
Country	US - United States
Keywords	amino acid ; ab initio methods ; empirical potentials
Subject RIV	CF - Physical ; Theoretical Chemistry
R&D Projects	GA203/05/0009 GA ČR - Czech Science Foundation (CSF)
	GD203/05/H001 GA ČR - Czech Science Foundation (CSF)
	IAA400550510 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR)
	LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
CEZ	AV0Z40550506 - UOCHB-X (2005-2011)
UT WOS	000265268800037
DOI	10.1021/ct800508v
Annotation	Interactions between amino acid side chains play a crucial role both within a folded protein and between the interacting protein molecules. Here we have selected a representative set of 24 of the 400 (20 × 20) possible interacting side chain pairs and computed the interaction energy in the gas phase using several different, commonly used, ab initio and force field methods, namely Møller-Plesset perturbation theory (MP2), density functional theory combined with symmetry-adapted perturbation theory (DFT-SAPT), density functional theory empirically augmented with an empirical dispersion term (DFT-D), and empirical potentials using the OPLS-AA/L and Amber03 force fields. All the methods were compared against a reference method taken to be the CCSD(T) level of theory extrapolated to the complete basis set limit. We found a high degree of agreement between the different methods, even though the range of binding energies obtained was extremely large.
Workplace	Institute of Organic Chemistry and Biochemistry
Contact	asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434
Year of Publishing	2009

Number of the records: 1