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CAVER Analyst

Current version:
Version Download
CAVER Analyst 1.0 All platforms

Software and hardware requirements

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

Important Notes

  • 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: "caver_analyst-macos_universal.zip 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.

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.


Data

Download
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 3.01 PyMOL Plugin 3.01 Download
All versions:
Version Download
CAVER 3.0 PyMOL Plugin BETA 1 3.0b1 Download

Older versions of CAVER PyMOL Plugin are available upon request.


Data

Download
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
Recommended citations:
CAVER Analyst Kozlíková, B., Šebestová, E., Šustr, V., Brezovský, J., Strnad, O., Daniel, L., Bednář, D., Pavelka, A., Maňák, M., Bezděka, M., Beneš, P., Kotry, M., Gora, A. W., Damborský, J., Sochor, J.: CAVER Analyst 1.0: Graphic Tool for Interactive Visualization and Analysis of Tunnels and Channels in Protein Structures, Bioinformatics, 30(18), 2014.
[BibTeX]
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]


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