About: Identifying stabilizing key residues in proteins using interresidue interaction energy matrix

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	We are proposing an interresidue interaction energy map (IEM) – a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. For the theoretical adjustment of the proposed method, we chose the Trp-cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical forcefield methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trpcage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. We are proposing an interresidue interaction energy map (IEM) – a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. For the theoretical adjustment of the proposed method, we chose the Trp-cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical forcefield methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trpcage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. (en) Navrhujeme využití interreziduální matice interakčních energií jako nástroj pro analýbu a bioinformatiku proteinů. Tato metoda využívá sumace párových interakcí dané aminokyseliny jako měřítka její strukturální důležitosti. Tento postup demonstrujeme na příkladu Trp-cage mini proteinu jako modelového sytému a srovnáváme různé druhy výpočetních metod. IEM metoda správně identifikovala tryptophane jako klíčové reziduum v tomto proteinu. (cs)
Title	Identifying stabilizing key residues in proteins using interresidue interaction energy matrix Identifikace klíčových reziduí pro stabilizaci proteinu použitím matice interakční energie (cs) Identifying stabilizing key residues in proteins using interresidue interaction energy matrix (en)
skos:prefLabel	Identifying stabilizing key residues in proteins using interresidue interaction energy matrix Identifikace klíčových reziduí pro stabilizaci proteinu použitím matice interakční energie (cs) Identifying stabilizing key residues in proteins using interresidue interaction energy matrix (en)
skos:notation	RIV/61388963:_____/08:00314780!RIV09-AV0-61388963
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GA203/05/0009), P(GA203/06/1727), P(GD203/05/H001), P(LC512), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	1
http://linked.open...vai/riv/dodaniDat	2009
http://linked.open...aciTvurceVysledku	Biedermannová, Lada Vondrášek, Jiří Hobza, Pavel
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	371314
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/08:00314780
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	protein stabilisation; an-initio calculation; interaction energy (en)
http://linked.open.../riv/klicoveSlovo	interaction energy protein stabilisation an-initio calculation
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[2B8C99AB1A75]
http://linked.open...i/riv/nazevZdroje	Proteins-Structure, Function and Bioinformatics
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	3 (xsd:int)
http://linked.open...vavai/riv/projekt	Center for biomolecules and complex molecular systems Experimental Study and Computer Modeling of the Structure and Function of the Complex Molecular Systems and Bio(macro)molecules Experimental and computational analysis of hydrophobic clusters in thermophilic proteins Structure and dynamics of DNA nitrogeneous bases, base pairs, oligonucleotides and their complexes with water, ions and drugs
http://linked.open...UplatneniVysledku	2008
http://linked.open...v/svazekPeriodika	72
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Vondrášek, Jiří Bendová, Lada
http://linked.open...ain/vavai/riv/wos	000256609800035
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	0887-3585
number of pages	12 (xsd:int)
is http://linked.open...avai/riv/vysledek of	Identifying stabilizing key residues in proteins using interresidue interaction energy matrix Identifying stabilizing key residues in proteins using interresidue interaction energy matrix Identifying stabilizing key residues in proteins using interresidue interaction energy matrix Identifying stabilizing key residues in proteins using interresidue interaction energy matrix

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