Publication details

Caver web: identification of tunnels and channels in proteins and analysis of ligand transport

Authors

ŠTOURAČ Jan VAVRA O. KOKKONEN Piia Pauliina FILIPOVIČ Jiří FONSECA PINTO Gabriela Filipa SCHENKMAYEROVÁ Andrea DAMBORSKÝ Jiří BEDNÁŘ David

Year of publication 2019
Type Conference abstract
MU Faculty or unit

Faculty of Science

Citation
Description Caver Web 1.0 is a novel interactive web server suitable for comprehensive analysis of protein tunnels or channels as well as the ligands’ transport through identified access pathways. Caver Web is the first web tool allowing both these analyses within a single graphical user interface. The server is built on top of the tunnel detection tool Caver and employs newly developed CaverDock to study the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for tunnel detection and optionally a list of ligands for transport analysis. The automated guidance procedures assist the users to correctly set up the calculation leading to accurate and biologically relevant results. The identified tunnels, their properties and energy profiles of passing ligands can be directly analyzed and visualized. The tool is very fast (2–20 min per job), making it suitable even for virtual screening. A simple setup and a comprehensible graphical user interface makes the tool accessible for broader scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.