Detail publikačního výsledku

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

MUSIL, M.; JEŽÍK, A.; HAMŠÍKOVÁ, M.; ŠTOURAČ, J.; GALGONEK, J.; EYRILMEZ, S.; VONDRÁŠEK, J.; DAMBORSKÝ, J.; BEDNÁŘ, D.

Original Title

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

English Title

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

Type

WoS Article

Original 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.

English 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.

Keywords

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

Key words in English

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

Authors

MUSIL, M.; JEŽÍK, A.; HAMŠÍKOVÁ, M.; ŠTOURAČ, J.; GALGONEK, J.; EYRILMEZ, S.; VONDRÁŠEK, J.; DAMBORSKÝ, J.; BEDNÁŘ, D.

RIV year

2023

Released

17.11.2022

Publisher

Elsevier

Location

Amsterdam

ISBN

2001-0370

Periodical

Computational and Structural Biotechnology Journal

Volume

20

Number

1

State

Kingdom of Sweden

Pages from

6512

Pages to

6518

Pages count

7

URL

https://reader.elsevier.com/reader/sd/pii/S2001037022005244?token=BBEEF236BF39C0CD3EA54616CE798E19BDF6535FBFF0E62B230291509E05B03E799D1DB6A7505295EF311EBB0DF71D21&originRegion=eu-west-1&originCreation=20230110080845

Full text in the Digital Library

http://hdl.handle.net/

BibTex

@article{BUT180689,
  author="Miloš {Musil} and Andrej {Ježík} and Marie {Hamšíková} and Jan {Štourač} and Jakub {Galgonek} and Saltuk Mustafa {Eyrilmez} and Jiří {Vondrášek} and Jiří {Damborský} and David {Bednář}",
  title="Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web",
  journal="Computational and Structural Biotechnology Journal",
  year="2022",
  volume="20",
  number="1",
  pages="6512--6518",
  doi="10.1016/j.csbj.2022.11.031",
  issn="2001-0370",
  url="https://reader.elsevier.com/reader/sd/pii/S2001037022005244?token=BBEEF236BF39C0CD3EA54616CE798E19BDF6535FBFF0E62B230291509E05B03E799D1DB6A7505295EF311EBB0DF71D21&originRegion=eu-west-1&originCreation=20230110080845"
}