CaverDock: A Novel Method for the Fast Analysis of Ligand Transport
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14610%2F20%3A00115044" target="_blank" >RIV/00216224:14610/20:00115044 - isvavai.cz</a>
Result on the web
<a href="https://ieeexplore.ieee.org/document/8674575" target="_blank" >https://ieeexplore.ieee.org/document/8674575</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1109/TCBB.2019.2907492" target="_blank" >10.1109/TCBB.2019.2907492</a>
Alternative languages
Result language
angličtina
Original language name
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport
Original language description
Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the access tunnel in such a way that the ligand movement is contiguous and the energy is minimized. The result of CaverDock calculation is a ligand trajectory and an energy profile of transport process. CaverDock uses the modified docking program Autodock Vina for molecular docking and implements a parallel heuristic algorithm for searching the space of possible trajectories. Our method lies in between the geometrical approaches and molecular dynamics simulations. Contrary to the geometrical methods, it provides an evaluation of chemical forces. However, it is far less computationally demanding and easier to set up compared to molecular dynamics simulations. CaverDock will find a broad use in the fields of computational enzymology, drug design and protein engineering. The software is available free of charge to the academic users at https://loschmidt.chemi.muni.cz/caverdock/.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
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>S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
IEEE/ACM Transactions on Computational Biology and Bioinformatics
ISSN
1545-5963
e-ISSN
1557-9964
Volume of the periodical
17
Issue of the periodical within the volume
5
Country of publishing house
US - UNITED STATES
Number of pages
14
Pages from-to
1625-1638
UT code for WoS article
000576418300015
EID of the result in the Scopus database
2-s2.0-85092801771