FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock 1.0. 2017. |
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Basic information | |
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Original name | CaverDock 1.0 |
Name in Czech | CaverDock 1.0 |
Authors | FILIPOVIČ, Jiří (203 Czech Republic, belonging to the institution), Ondřej VÁVRA (203 Czech Republic, belonging to the institution), Jan PLHÁK (203 Czech Republic, belonging to the institution), David BEDNÁŘ (203 Czech Republic, belonging to the institution), Sérgio Manuel MARQUES (620 Portugal, belonging to the institution), Jan BREZOVSKÝ (203 Czech Republic, belonging to the institution), Luděk MATYSKA (203 Czech Republic, belonging to the institution) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution). |
Edition | 2017. |
Other information | |
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Original language | English |
Type of outcome | Software |
Field of Study | 10201 Computer sciences, information science, bioinformatics |
Country of publisher | Czech Republic |
Confidentiality degree | is not subject to a state or trade secret |
WWW | URL |
RIV identification code | RIV/00216224:14610/17:00098438 |
Organization unit | Institute of Computer Science |
Keywords in English | CaverDock;transport processes in proteins |
Technical parameters | Software je dokončen a uvolněn uživatelům na adrese: https://loschmidt.chemi.muni.cz/caverdock/ kontaktní osoba prof. Damborský, UKB-Kamenice 5/A13, Brno 62500, tel.549493467, jiri@chemi.muni.cz |
Tags | rivok |
Tags | International impact |
Changed by | Changed by: prof. Mgr. Jiří Damborský, Dr., učo 1441. Changed: 1/3/2019 11:24. |
Abstract |
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CaverDock is a software tool for rapid analysis of transport processes in proteins. It models the transportation of a ligand - a substrate, a product, an inhibitor, a co-factor or a co-solvent - from outside environment into the protein active or binding site and vice versa. The input for the calculation is a protein structure in PDB format and a ligand structure in the PDBQ format. The outputs are ligand’s trajectory and energetic profile. CaverDock implements a novel algorithm which is based on molecular docking and is able to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. The current version of CaverDock uses CAVER for pathway identification and heavily modified Autodock Vina as a docking engine. The tool is much faster than molecular dynamic simulations (2-20 min per job), making it suitable even for virtual screening. The software is extremely easy to use as it requires in its minimalistic configuration the setup for AutoDock Vina and geometry of the tunnel. |
Abstract (in Czech) |
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CaverDock je softwareový nástroj pro rychlou analýzu transportních procesů v proteinech. Modeluje transport ligandu - substrátu, produktu, inhibitoru, ko-factoru či ko-solventu - z vnějšího prostředí do aktivního/vazebného místa v proteinu či opačným směrem. Vstupem pro výpočet jsou struktury proteinu a ligandu v PDBQT formátu. Výstupem je trajektorie ligandu a energetický profil. CaverDock implementuje zcela nový algoritmus založený na molekulovém dockingu, který je schopen vypočítat souvislou trajektorii ligandu a odhadnout energii jeho transportu. Současná verze CaverDocku používá CAVER pro identifikaci cesty v proteinu a výrazně modifikovaný AutoDock Vina jako dokovací engine. Nástroj je mnohem rychlejší než simulace pomocí molekulové dynamiky (2-20min na úlohu), což jej činní vhodný pro virtuální screening. Software je velmi jednoduchý na použití, jelikož v minimalistické konfiguraci vyžaduje pouze nastavení pro AutoDock Vina a geometrii tunelu. |
Links | |
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MUNI/M/1888/2014, interní kód MU | Name: Pokročilé hybridní metody studia transportních procesů v proteinech a jejich využití v designu biokatalyzátorů |
Investor: Masaryk University, INTERDISCIPLINARY - Interdisciplinary research projects |
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