CAVER pipeline

CAVER specifications

Information


Unique identifier OMICS_04690
Name CAVER
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainers


  • person_outline Jiri Damborsky <>
  • person_outline Barbora Kozlikova <>

Publications for CAVER

CAVER IN pipelines

 (4)
2016
PMCID: 4735121
PMID: 26829126
DOI: 10.1371/journal.pone.0147761

[…] interactions were set to 10.0 å. the shake algorithm was used for the covalent bonds involving hydrogen [47]. the trajectory of md simulation was analyzed for the structure stability., the program caver 3.0 was used for of access tunnel computation [48]. the x-ray structures were used as input files for caver to find potential access tunnels involved in ligand egress. all the structures […]

2016
PMCID: 4735121
PMID: 26829126
DOI: 10.1371/journal.pone.0147761

[…] the trajectory of md simulation was analyzed for the structure stability., the program caver 3.0 was used for of access tunnel computation [48]. the x-ray structures were used as input files for caver to find potential access tunnels involved in ligand egress. all the structures and access tunnels presented in this paper were visualized and rendered in pymol 1.6. the sphere representation […]

2011
PMCID: 3141018
PMID: 21811565
DOI: 10.1371/journal.pone.0022134

[…] modeling of the sceosc enzyme wild type and of the mutants; b) anm (anisotropic network model) for the analysis of vibrational motions (http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi); c) caver (http://loschmidt.chemi.muni.cz/caver/index.php) for identifying and visualizing routes from the interior of the protein to the bulk solvent and d) pymol (http://pymol.sourceforge.net/) […]

2011
PMCID: 3141018
PMID: 21811565
DOI: 10.1371/journal.pone.0022134

[…] type and of the mutants; b) anm (anisotropic network model) for the analysis of vibrational motions (http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi); c) caver (http://loschmidt.chemi.muni.cz/caver/index.php) for identifying and visualizing routes from the interior of the protein to the bulk solvent and d) pymol (http://pymol.sourceforge.net/) for visualization and figures preparation., […]

CAVER institution(s)
Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Brno, Czech Republic; Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Plzen, Czech Republic

CAVER review

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mamapcr

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Desktop
good