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

Kód výsledku v 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>

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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

Název v anglickém jazyce

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

Popis výsledku anglicky

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

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CE - Biochemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

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

Rok uplatnění

2008

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Information and Modeling

ISSN

1549-9596

e-ISSN

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Svazek periodika

48

Číslo periodika v rámci svazku

11

Stát vydavatele periodika

CZ - Česká republika

Počet stran výsledku

8

Strana od-do

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Kód UT WoS článku

000261103700013

EID výsledku v databázi Scopus

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