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Statements

Subject Item
n2:RIV%2F61388963%3A_____%2F09%3A00324799%21RIV09-AV0-61388963
rdf:type
n12:Vysledek skos:Concept
dcterms:description
Interakce mezi aminokyselinami hrají zásadní roli ve stabilizaci a interakci proteinů. V této práci na reprezentativním souboru 24 párů (z celkového počtu 400) aminokyselin prezentujeme interakční enegii ve vakuu získanou několika různými výpočetními metodami: konkrétně MP2, DFT-SAPT, DFT-D a OPLS-AA/L a Amber03 empirickými potenciály. Všechny metody byly srovnány s referenčními hodnotami získanými CCSD(T) extrapolovanými na nekonečnou bázi. Nalezli jsme vysokou míru korelace pro širokou škálu interakčních energií u všech použitých metod, přestože rozsah hodnot byl extrémně široký. 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. 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.
dcterms:title
Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures Reprezentativní interakce aminokyselin v proteinech: srovnání přesných ab-initio kvantově chemických výpočtů s empirickými potenciály
skos:prefLabel
Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures Reprezentativní interakce aminokyselin v proteinech: srovnání přesných ab-initio kvantově chemických výpočtů s empirickými potenciály
skos:notation
RIV/61388963:_____/09:00324799!RIV09-AV0-61388963
n3:aktivita
n11:Z n11:P
n3:aktivity
P(GA203/05/0009), P(GD203/05/H001), P(IAA400550510), P(LC512), Z(AV0Z40550506)
n3:cisloPeriodika
4
n3:dodaniDat
n13:2009
n3:domaciTvurceVysledku
n14:4936094 n14:2932016 n14:7358946
n3:druhVysledku
n16:J
n3:duvernostUdaju
n7:S
n3:entitaPredkladatele
n9:predkladatel
n3:idSjednocenehoVysledku
339016
n3:idVysledku
RIV/61388963:_____/09:00324799
n3:jazykVysledku
n15:eng
n3:klicovaSlova
amino acid; ab initio methods; empirical potentials
n3:klicoveSlovo
n4:empirical%20potentials n4:ab%20initio%20methods n4:amino%20acid
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[011F0AD2A3EC]
n3:nazevZdroje
Journal of Chemical Theory and Computation
n3:obor
n17:CF
n3:pocetDomacichTvurcuVysledku
3
n3:pocetTvurcuVysledku
5
n3:projekt
n10:IAA400550510 n10:LC512 n10:GA203%2F05%2F0009 n10:GD203%2F05%2FH001
n3:rokUplatneniVysledku
n13:2009
n3:svazekPeriodika
5
n3:tvurceVysledku
Hobza, Pavel Riley, K. E. Laskowski, R. Vondrášek, Jiří Berka, Karel
n3:wos
000265268800037
n3:zamer
n18:AV0Z40550506
s:issn
1549-9618
s:numberOfPages
11