CaverDock is a software tool for rapid analysis of transport processes in proteins [1,2]. It models the transportation of a ligand - a substrate, a product, an inhibitor, a co-factor or a co-solvent - from outside environment into the protein active or binding site and vice versa.
The input for the calculation is a protein structure in PDB format and a ligand structure in the PDBQ format. The outputs are ligand’s trajectory and energetic profile. CaverDock implements a novel algorithm which is based on molecular docking and is able to produce contiguous ligand trajectory and estimation of a binding energy along the pathway.
The current version of CaverDock uses Caver  for pathway identification and heavily modified Autodock Vina  as a docking engine. The tool is much faster than molecular dynamic simulations (2-20 min per job), making it suitable even for virtual screening. The software is extremely easy to use as it requires in its minimalistic configuration the setup for AutoDock Vina and geometry of the tunnel.
CaverDock can be either downloaded as a standalone command-line executable (links below) or used via user-friendly web interface Caver Web.
- Vavra, O., Filipovic, J., Plhak, J., Bednar, D., Marques, S. M., Brezovsky, J., Stourac, J., Matyska, L., Damborsky, J., 2019: CaverDock: A Molecular Docking-Based Tool to Analyse Ligand Transport through Protein Tunnels and Channels. Bioinformatics. DOI: 10.1093/bioinformatics/btz386.
- Filipovic, J., Vavra, O., Plhak, J., Bednar, D., Marques, S. M., 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. DOI: 10.1109/TCBB.2019.2907492.
- Pinto, G. P., Vavra, O., Filipovic, J., Stourac, J., Bednar, D., Damborsky, J., Fast Screening of Inhibitor Binding/Unbinding using Novel Software Tool CaverDock. Submitted, Visual supplement available here.
- Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J., Damborsky, J., 2012: CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures. PLOS Computational Biology 8: e1002708.
- Trott, O., Olson, A.J., 2010: AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization and Multithreading. Journal of Computational Chemistry 31: 455-461.
- This work was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047) including access to computing and storage facilities.
- Supported by the European Regional Development Fund - Project INBIO (No. CZ.02.1.01/0.0/0.0/16_026/0008451)