CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F19%3A00072473" target="_blank" >RIV/00159816:_____/19:00072473 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14310/19:00110114

Výsledek na webu

<a href="https://academic.oup.com/bioinformatics/article-abstract/35/23/4986/5488163?redirectedFrom=fulltext" target="_blank" >https://academic.oup.com/bioinformatics/article-abstract/35/23/4986/5488163?redirectedFrom=fulltext</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/bioinformatics/btz386" target="_blank" >10.1093/bioinformatics/btz386</a>

Jazyk výsledku

angličtina

Název v původním jazyce

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels

Popis výsledku v původním jazyce

Motivation: Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins&apos; external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. Results: CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock&apos;s usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering.

Název v anglickém jazyce

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels

Popis výsledku anglicky

Motivation: Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins&apos; external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. Results: CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock&apos;s usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

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)

Rok uplatnění

2019

Kód důvěrnosti údajů

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

Název periodika

Bioinformatics

ISSN

1367-4803

e-ISSN

—

Svazek periodika

35

Číslo periodika v rámci svazku

23

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

8

Strana od-do

4986-4993

Kód UT WoS článku

000506808900016

EID výsledku v databázi Scopus

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