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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F08%3A00024957%21RIV10-MSM-14310___
rdf:type
n12:Vysledek skos:Concept
dcterms: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.
dcterms: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
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
skos:notation
RIV/00216224:14310/08:00024957!RIV10-MSM-14310___
n3:aktivita
n4:Z n4:P
n3:aktivity
P(GA303/06/0570), P(LC06030), Z(MSM0021622413)
n3:cisloPeriodika
11
n3:dodaniDat
n5:2010
n3:domaciTvurceVysledku
n7:5522064 n7:4347374 n7:7678037 n7:9309616 n7:3993779
n3:druhVysledku
n16:J
n3:duvernostUdaju
n17:S
n3:entitaPredkladatele
n11:predkladatel
n3:idSjednocenehoVysledku
371756
n3:idVysledku
RIV/00216224:14310/08:00024957
n3:jazykVysledku
n10:eng
n3:klicovaSlova
lectins; molecular modeling; computational chemistry; in silico prediction; docking
n3:klicoveSlovo
n9:lectins n9:molecular%20modeling n9:docking n9:in%20silico%20prediction n9:computational%20chemistry
n3:kodStatuVydavatele
CZ - Česká republika
n3:kontrolniKodProRIV
[DBF4B59032DF]
n3:nazevZdroje
Journal of Chemical Information and Modeling
n3:obor
n18:CE
n3:pocetDomacichTvurcuVysledku
5
n3:pocetTvurcuVysledku
5
n3:projekt
n13:LC06030 n13:GA303%2F06%2F0570
n3:rokUplatneniVysledku
n5:2008
n3:svazekPeriodika
48
n3:tvurceVysledku
Wimmerová, Michaela Kříž, Zdeněk Koča, Jaroslav Prokop, Martin Adam, Jan
n3:wos
000261103700013
n3:zamer
n19:MSM0021622413
s:issn
1549-9596
s:numberOfPages
8
n14:organizacniJednotka
14310