About: Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	The interactions between amino acid side chains in proteins are generally considered to be the most important stabilizing factor controlling the precise arrangement of the polypeptide chain into a well-defined spatial structure. We used the RI-DFT-D method to calculate the full 20 20 matrix of interaction energies between all pairs of amino acid side chains. We find that all of the calculated interaction energies between selected pairs of amino acids are attractive in the gas phase with the exception of side chain pairs having the same total charge. We compared these data with those calculated by the parm03 and OPLS-AA/L force fields to investigate the reliability of simple methods in modeling biomolecules and their behavior. The force fields yield good overall interaction energies for our set but have problems in evaluation of some particular interactions which could be of principal importance for protein stability. The interactions between amino acid side chains in proteins are generally considered to be the most important stabilizing factor controlling the precise arrangement of the polypeptide chain into a well-defined spatial structure. We used the RI-DFT-D method to calculate the full 20 20 matrix of interaction energies between all pairs of amino acid side chains. We find that all of the calculated interaction energies between selected pairs of amino acids are attractive in the gas phase with the exception of side chain pairs having the same total charge. We compared these data with those calculated by the parm03 and OPLS-AA/L force fields to investigate the reliability of simple methods in modeling biomolecules and their behavior. The force fields yield good overall interaction energies for our set but have problems in evaluation of some particular interactions which could be of principal importance for protein stability. (en)
Title	Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins (en)
skos:prefLabel	Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins (en)
skos:notation	RIV/61388963:_____/10:00351179!RIV11-GA0-61388963
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GAP208/10/0725), P(LC512), Z(AV0Z40550506), Z(MSM6198959216)
http://linked.open...iv/cisloPeriodika	7
http://linked.open...vai/riv/dodaniDat	2011
http://linked.open...aciTvurceVysledku	Vondrášek, Jiří
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	257189
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/10:00351179
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	protein structure; DFT method; force fields; interaction energy (en)
http://linked.open.../riv/klicoveSlovo	protein structure DFT method force fields interaction energy
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[465BB2CC89F6]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	Center for biomolecules and complex molecular systems Studium mezimolekulových interakcí v molekulových krystalech a proteinech
http://linked.open...UplatneniVysledku	2010
http://linked.open...v/svazekPeriodika	6
http://linked.open...iv/tvurceVysledku	Vondrášek, Jiří Berka, K. Hobza, P. Laskowski, R. A.
http://linked.open...ain/vavai/riv/wos	000279751500026
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství Modulation of signalling and regulatory pathways in normal and cancer cells
issn	1549-9618
number of pages	13 (xsd:int)
is http://linked.open...avai/riv/vysledek of	Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

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