CAVER Analyst

Current version:
Version Download
CAVER Analyst 2.0 (BETA 2) 2.0 All platforms
All versions:
Version Download
CAVER Analyst 2.0 (BETA) 2.0 Download (64-bit)
CAVER Analyst 2.0 (BETA) 2.0 Download (32-bit)
CAVER Analyst 1.0 1.0 All platforms

Software and hardware requirements

Minimum configuration:
  • Java 1.8 (Java 1.7 for Analyst 1.0)
  • 2 GB RAM
  • Intel HD family graphics adapter
Recommended configuration:
  • Windows 7 x64
  • Java 1.8 x64
  • 8 GB RAM
  • AMD/ATI Radeon or nVIDIA GeForce family graphics card

Important Notes

  • When using Windows a message "Windows Defender SmartScreen prevented an unrecognized app from starting. Running this app might put your PC at risk." may appear. This is caused by the fact that the application is currently unsigned. To sove this issue simply click at More info and then Run anyway. For more information reffer to Windows Defender SmartScreen.
  • If you are using Java 1.7 and Windows 7, downloading files from PDB database might not work due to an error in the Windows firewall. The way to work this around is to run following command from your Windows command line with administrator rights: netsh advfirewall set global StatefulFTP disable.
  • Message: " is damaged and can't be opened. You should move it to the Trash." This message can occur when unzipping the CAVER Analyst on the MacOS system version 10.8 Snow Leopard and later. The problem is connected to the security settings of the system since the application does not come from the App Store. It you face this problem, please refer to this page The General pane of Security & Privacy preferences or contact your system administrator.

Changelog - CAVER Analyst 2.0 (BETA 2)


  • Enabled changing of maximum application memory from Application Settings


  • Fixed error when opening Application Settings while running on Java 9
  • Fixed cavities not rendering on some Intel HD GPUs
Click here to see the full change log (including older versions).

CAVER (command line version)

Current version:
Version Download
CAVER 3.02 3.02 Download
All versions:
Version Download
CAVER 3.03 (BETA) 3.03 Download
CAVER 3.01 3.01 Download
CAVER 3.0 3.0 Download
CAVER 3.0 BETA (for PLoS) 3.0 Download

About CAVER 3.03 BETA

  • This version uses additively weighted Voronoi diagram. It is possible to return to the previously used ordinary Voronoi diagram by the parameter “awvd no”.
  • Memory requirements and computational times have significantly decreased. This can be useful for the analysis of large structures, e.g., hundred thousands of atoms.
  • Utilization of additively weighted Voronoi diagram did not change significantly the properties of tunnel clusters in molecular dynamics trajectory of haloalkane dehalogenase DhaA. However, the properties and ordering of individual tunnels in static structures may change, which is due to a principal limitation of geometry based analysis of tunnels in static structures. If your conclusions are sensitive to small changes in tunnel radii or lengths, we strongly recommend to analyse a molecular dynamics trajectory rather than a single static structure.
  • A new parameter was added: parallel yes|no. Voronoi diagram computation uses multiple processor cores, unless this parameter is set to no. Note that Java may still use multiple cores, e.g., for garbage collection, which has to be solved on the operating system level. In Linux, taskset can be used for this purpose. For example the command taskset -c 0,3,4 java -jar caver.jar -<other arguments> uses only CPU cores 0, 3 and 4. Scripts in the directory caver_3.0.3/caver/scripts shows automated solution for the PBS environment.

The main difference between CAVER 3.01 and CAVER 3.02 versions is the following:

  • More efficient version of UPGMA clustering algorithm is available and used as default. Previous version can still be used by setting 'clustering_algorithm' to 'loewenstein' (default is the efficient algorithm - 'murtagh'). Disc space is no longer needed to store distance matrix. Clustering speed benefits from large RAM (and accordingly set java -Xmx values).

The main differences between CAVER 3.0 and CAVER 3.01 versions are the following:

  • The starting point optimization procedure was corrected. Previously, the starting vertex was sometimes identified in a too narrow cavity. The change can lead to minor changes in the geometric properties of tunnels, similarly as if the parameter seed is modified.
  • Three letters were originally expected for the residue name while reading the PDB files (columns 18 - 20). This complies with the PDB file Format Guide, however, some structures use four letters (columns 18 - 21). CAVER now reads four letters as default, but it is possible to return to the three letter mode by setting ‘long_residue_names’ to ‘no’.
  • The atom serial number can be newly composed of the letters as well as the digits. In such cases, letters are interpreted as additional digits 10, 11, 12, etc. This is useful when loading large PDB files.

Older versions of CAVER are available upon request.


Molecular dynamics simulation of haloalkane dehalogenase enzyme DhaA - 20,000 snapshots in PDB files Download
PyMOL session for the clusters of tunnels of haloalkane dehalogenase enzyme DhaA Download
PyMOL session for tunnels of structure with PDB ID 1MXT Download

CAVER 3.0 PyMOL plugin

Current version:
Version Download
CAVER 3.0.3 PyMOL Plugin 3.0.3 Download
All versions:
Version Download
CAVER 3.0.1 PyMOL Plugin 3.0.1 Download
CAVER 3.0 PyMOL Plugin BETA 1 3.0b1 Download

Older versions of CAVER PyMOL Plugin are available upon request.


Molecular dynamics simulation of haloalkane dehalogenase enzyme DhaA - 20,000 snapshots in PDB files Download
PyMOL session for the clusters of tunnels of haloalkane dehalogenase enzyme DhaA Download
PyMOL session for tunnels of structure with PDB ID 1MXT Download

CaverDock 1.0

Current version:
Version Download
Binaries for Ubuntu 18.04 LTS 1.2 Download
Apptainer/Singularity Image 1.2 Download

CaverDock is a software tool for rapid analysis of transport processes in proteins. 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.

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.
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.
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.

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