About: In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL

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About: In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	This article is focused on the application of two types of AutoDock and DOCK docking software, and aimed at studying the interaction of a calcium-dependent bacterial lectin PA-IIL from Pseudomonas aeruginosa as well as its mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure. The results of DOCK were further optimized by molecular dynamics and rescored using AMBER. For both software, the agreement of the docked structures and the provided binding energies were evaluated in terms of prediction accuracy. This was carried out by comparing the computed results to the crystal structures and experimentally determined binding energies, respectively. The performance of the both docking software applied on studied problem was evaluated as well. This article is focused on the application of two types of AutoDock and DOCK docking software, and aimed at studying the interaction of a calcium-dependent bacterial lectin PA-IIL from Pseudomonas aeruginosa as well as its mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure. The results of DOCK were further optimized by molecular dynamics and rescored using AMBER. For both software, the agreement of the docked structures and the provided binding energies were evaluated in terms of prediction accuracy. This was carried out by comparing the computed results to the crystal structures and experimentally determined binding energies, respectively. The performance of the both docking software applied on studied problem was evaluated as well. (en)
Title	In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies (en)
skos:prefLabel	In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies (en)
skos:notation	RIV/00216224:14310/08:00024957!RIV10-MSM-14310___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GA303/06/0570), P(LC06030), Z(MSM0021622413)
http://linked.open...iv/cisloPeriodika	11
http://linked.open...vai/riv/dodaniDat	2010
http://linked.open...aciTvurceVysledku	Prokop, Martin Adam, Jan Koča, Jaroslav Wimmerová, Michaela Kříž, Zdeněk
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	Masarykova univerzita / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	371756
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/08:00024957
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	lectins; molecular modeling; computational chemistry; in silico prediction; docking (en)
http://linked.open.../riv/klicoveSlovo	lectins docking molecular modeling computational chemistry in silico prediction
http://linked.open...odStatuVydavatele	CZ - Česká republika
http://linked.open...ontrolniKodProRIV	[DBF4B59032DF]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Information and Modeling
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	5 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Biomolecular centre Structure-function studies on lectins and adhesins from microbial patogens
http://linked.open...UplatneniVysledku	2008
http://linked.open...v/svazekPeriodika	48
http://linked.open...iv/tvurceVysledku	Adam, Jan Koča, Jaroslav Wimmerová, Michaela Prokop, Martin Kříž, Zdeněk
http://linked.open...ain/vavai/riv/wos	000261103700013
http://linked.open...n/vavai/riv/zamer	Proteiny v metabolismu a při interakci organismů s prostředím
issn	1549-9596
number of pages	8 (xsd:int)
http://localhost/t...ganizacniJednotka	14310

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