CaverDock

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 [3] for pathway identification and heavily modified Autodock Vina [4] 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.

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References

  1. Vavra, O., Filipovic, J., Plhak, J., Bednar, D., Marques, S., Brezovsky, J., Pavelka, A., Matyska, L., Damborsky, J., CAVERDOCK: A New Tool for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. In preparation.
  2. Filipovic, J., Vavra, O., Plhak, J., Bednar, D., Marques, S., Brezovsky, J., Matyska, L., Damborsky, J., A Novel Method for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. In preparation.
  3. 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.
  4. 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.