Cargando…

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

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 b...

Descripción completa

Detalles Bibliográficos
Autores principales: Musil, Milos, Jezik, Andrej, Jankujova, Marie, Stourac, Jan, Galgonek, Jakub, Mustafa Eyrilmez, Saltuk, Vondrasek, Jiri, Damborsky, Jiri, Bednar, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9705369/
https://www.ncbi.nlm.nih.gov/pubmed/36467577
http://dx.doi.org/10.1016/j.csbj.2022.11.031
_version_ 1784840268533465088
author Musil, Milos
Jezik, Andrej
Jankujova, Marie
Stourac, Jan
Galgonek, Jakub
Mustafa Eyrilmez, Saltuk
Vondrasek, Jiri
Damborsky, Jiri
Bednar, David
author_facet Musil, Milos
Jezik, Andrej
Jankujova, Marie
Stourac, Jan
Galgonek, Jakub
Mustafa Eyrilmez, Saltuk
Vondrasek, Jiri
Damborsky, Jiri
Bednar, David
author_sort Musil, Milos
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9705369
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Research Network of Computational and Structural Biotechnology
record_format MEDLINE/PubMed
spelling pubmed-97053692022-12-02 Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web Musil, Milos Jezik, Andrej Jankujova, Marie Stourac, Jan Galgonek, Jakub Mustafa Eyrilmez, Saltuk Vondrasek, Jiri Damborsky, Jiri Bednar, David Comput Struct Biotechnol J Research Article 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. Research Network of Computational and Structural Biotechnology 2022-11-17 /pmc/articles/PMC9705369/ /pubmed/36467577 http://dx.doi.org/10.1016/j.csbj.2022.11.031 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Article
Musil, Milos
Jezik, Andrej
Jankujova, Marie
Stourac, Jan
Galgonek, Jakub
Mustafa Eyrilmez, Saltuk
Vondrasek, Jiri
Damborsky, Jiri
Bednar, David
Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web
title Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web
title_full Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web
title_fullStr Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web
title_full_unstemmed Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web
title_short Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web
title_sort fully automated virtual screening pipeline of fda-approved drugs using caver web
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9705369/
https://www.ncbi.nlm.nih.gov/pubmed/36467577
http://dx.doi.org/10.1016/j.csbj.2022.11.031
work_keys_str_mv AT musilmilos fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb
AT jezikandrej fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb
AT jankujovamarie fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb
AT stouracjan fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb
AT galgonekjakub fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb
AT mustafaeyrilmezsaltuk fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb
AT vondrasekjiri fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb
AT damborskyjiri fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb
AT bednardavid fullyautomatedvirtualscreeningpipelineoffdaapproveddrugsusingcaverweb