Frequently Asked Questions

Content

  1. How to cite CAVER?
  2. Which platforms are supported?
  3. How do I decide which atom to pick as the ' starting_point_atom ' and how many atoms to pick for a good analysis?

1. How to cite CAVER?

Recommended citations:
CAVER Analyst Jurcik, A., Bednar, D., Byska, J., Marques, S. M., Furmanova, K., Daniel, L., Kokkonen, P., Brezovsky, J., Strnad, O., Stourac, J., Pavelka, A., Manak, M., Damborsky, J., Kozlikova, B. : CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories., Bioinformatics, bty386, 2018.
CAVER, CAVER Plugin Chovancová,E., Pavelka, A., Beneš, P., Strnad, O., Brezovský, J., Kozlíková, B., Gora, A., Šustr, V., Klvaňa, M., Medek, P., Biedermannová, L., Sochor, J., Damborský, J.: CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures, PLoS Computational Biology 8: e1002708, 8(10), 2012.
[BibTeX]
CAVER, CAVER Plugin Pavelka, A., Šebestová, E., Kozlíková, B., Brezovský, J., Sochor, J., Damborský, J.: CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(3), 2016.
[BibTeX]
CaverDock 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, 2018.

2. Which platforms are supported?

Current version of CAVER Analyst plugin is available for Windows, Linux and MacOS X.

3. How do I decide which atom to pick as the ' starting_point_atom ' and how many atoms to pick for a good analysis?

CAVER is dedicated to finding and characterization of potential paths, which can be used by small molecules to travel to and from a burried site. The best position for starting point is usually in this site. It can be specified by atoms or residues around so that their geometric center lies in this site. If a ligand or cofactor is present, their residue ID or a selected atom might be suitable. CAVER will then optimize the geometric center so that it lies in free space, avoiding the cofactor. In case of ligand, you might want to use parameter exclude_residue_ids. In any case, you will see the starting point in the end.



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