CaverDock: A Novel Method for the Fast Analysis of Ligand Transport

Authors

Filipovic, J., Vavra, O., Plhak, J., Bednar, D., Marques, S., Brezovsky, J., Matyska, L., Damborsky, J.

Source

IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 17: 1625-1638 (2019)

Abstract

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 the 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 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/.

Full text

Citation

Filipovic, J., Vavra, O., Plhak, J., Bednar, D., Marques, S., Brezovsky, J., Matyska, L., Damborsky, J., 2019: CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM Transactions on Computational Biology and Bioinformatics 17: 1625-1638.

Martin Toul Won Doctorandus Prize of the Czech Head Award
Martin Toul Received the Award of the Ministry of Education, Youth and Sports for Outstanding Students
David Presented at ELIXIR 3D-BioInfo conference
2nd Place in the Competition of Transfera Technology Day 2023
Martin to Be a Chairperson at the 34th European Crystallography Congress 2024
Vice-Rector’s Award for Martin Toul
Veronika Presented at the 15th World Stroke Congress