Publication Details

Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web

MUSIL Miloš, JEŽÍK Andrej, HAMŠÍKOVÁ Marie, ŠTOURAČ Jan, GALGONEK Jakub, EYRILMEZ Saltuk Mustafa, VONDRÁŠEK Jiří, DAMBORSKÝ Jiří and BEDNÁŘ David. Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web. Computational and Structural Biotechnology Journal, vol. 20, no. 1, 2022, pp. 6512-6518. ISSN 2001-0370.
Czech title
Plně automatizovaný virutální screening FDA-schválených léčiv za využití Caver webu
Type
journal article
Language
english
Authors
Musil Miloš, Ing., Ph.D. (DIFS FIT BUT)
Ježík Andrej, Bc. (FIT BUT)
Hamšíková Marie (LL)
Štourač Jan (LL)
Galgonek Jakub (CAS CR)
Eyrilmez Saltuk Mustafa (LL)
Vondrášek Jiří (CAS CR)
Damborský Jiří, prof. Mgr., Dr. (LL)
Bednář David, Mgr. (LL)
URL
Keywords

Caver, CaverDock, FDA-approved drug, Channel, Tunnel, Virtual screening

Abstract

Protein tunnels are essential in transporting small molecules into the active sites of enzymes. Tunnels' geometrical and physico-chemical properties influence the transport process. The tunnels are attractive hot spots for protein engineering and drug development. However, studying the ligand binding and unbinding using experimental techniques is challenging, while in silico methods come with their limitations, especially in the case of resource-demanding virtual screening pipelines. Caver Web 1.2 is a new version of the web server combining the capabilities for the detection of protein tunnels with the calculation of the ligand trajectories. The new version of the Caver Web server was expanded with the ability to fetch novel ligands from the Integrated Database of Small Molecules and with the fully automated virtual screening pipeline allowing for the fast evaluation of the predefined set of over 4,300 currently approved drugs. The virtual screening pipeline is accompanied by a comprehensive user interface, making it a viable service for the broader spectrum of companies and the academic user community. The web server is freely available for academic use at https://loschmidt.chemi.muni.cz/caverweb.

Published
2022
Pages
6512-6518
Journal
Computational and Structural Biotechnology Journal, vol. 20, no. 1, ISSN 2001-0370
Publisher
Research Network of Computational and Structural Biotechnology
DOI
10.1016/j.csbj.2022.11.031
EID Scopus
2-s2.0-85142724459
BibTeX 
@ARTICLE{FITPUB12915,
   author = "Milo\v{s} Musil and Andrej Je\v{z}\'{i}k and Marie Ham\v{s}\'{i}kov\'{a} and Jan \v{S}toura\v{c} and Jakub Galgonek and Mustafa Saltuk Eyrilmez and Ji\v{r}\'{i} Vondr\'{a}\v{s}ek and Ji\v{r}\'{i} Damborsk\'{y} and David Bedn\'{a}\v{r}",
   title = "Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web",
   pages = "6512--6518",
   journal = "Computational and Structural Biotechnology Journal",
   volume = 20,
   number = 1,
   year = 2022,
   ISSN = "2001-0370",
   doi = "10.1016/j.csbj.2022.11.031",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/12915"
}
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