| Attributes | Values |
|---|
| rdf:type
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| 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. (cs)
- 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. (en)
|
| 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 (en)
- Reprezentativní interakce aminokyselin v proteinech: srovnání přesných ab-initio kvantově chemických výpočtů s empirickými potenciály (cs)
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| 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 (en)
- Reprezentativní interakce aminokyselin v proteinech: srovnání přesných ab-initio kvantově chemických výpočtů s empirickými potenciály (cs)
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| skos:notation
| - RIV/61388963:_____/09:00324799!RIV09-AV0-61388963
|
| http://linked.open...avai/riv/aktivita
| |
| http://linked.open...avai/riv/aktivity
| - P(GA203/05/0009), P(GD203/05/H001), P(IAA400550510), P(LC512), Z(AV0Z40550506)
|
| http://linked.open...iv/cisloPeriodika
| |
| http://linked.open...vai/riv/dodaniDat
| |
| http://linked.open...aciTvurceVysledku
| |
| http://linked.open.../riv/druhVysledku
| |
| http://linked.open...iv/duvernostUdaju
| |
| http://linked.open...titaPredkladatele
| |
| http://linked.open...dnocenehoVysledku
| |
| http://linked.open...ai/riv/idVysledku
| - RIV/61388963:_____/09:00324799
|
| http://linked.open...riv/jazykVysledku
| |
| http://linked.open.../riv/klicovaSlova
| - amino acid; ab initio methods; empirical potentials (en)
|
| http://linked.open.../riv/klicoveSlovo
| |
| http://linked.open...odStatuVydavatele
| - US - Spojené státy americké
|
| http://linked.open...ontrolniKodProRIV
| |
| http://linked.open...i/riv/nazevZdroje
| - Journal of Chemical Theory and Computation
|
| http://linked.open...in/vavai/riv/obor
| |
| http://linked.open...ichTvurcuVysledku
| |
| http://linked.open...cetTvurcuVysledku
| |
| http://linked.open...vavai/riv/projekt
| |
| http://linked.open...UplatneniVysledku
| |
| http://linked.open...v/svazekPeriodika
| |
| http://linked.open...iv/tvurceVysledku
| - Hobza, Pavel
- Vondrášek, Jiří
- Riley, K. E.
- Berka, Karel
- Laskowski, R.
|
| http://linked.open...ain/vavai/riv/wos
| |
| http://linked.open...n/vavai/riv/zamer
| |
| issn
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| number of pages
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