In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F08%3A00024957" target="_blank" >RIV/00216224:14310/08:00024957 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies

Original language 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 bothsoftware, 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. The molecular docking methods proved efficient in identifying the correct binding modes in terms of geometry, and partiall

Czech name

In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies

Czech 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 bothsoftware, 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. The molecular docking methods proved efficient in identifying the correct binding modes in terms of geometry, and partiall

Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2008

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Chemical Information and Modeling

ISSN

1549-9596

e-ISSN

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Volume of the periodical

48

Issue of the periodical within the volume

11

Country of publishing house

CZ - CZECH REPUBLIC

Number of pages

8

Pages from-to

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UT code for WoS article

000261103700013

EID of the result in the Scopus database

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