PyMOL Wiki - User contributions [en]

Caver2

2010-11-09T08:56:38Z

Hci:

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:ukazky-plugin.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:ukazky.png|1200px]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:

Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0]", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"[http://decibel.fi.muni.cz/download/papers/medek08.pdf Computation of tunnels in protein molecules using delaunay triangulation]". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

Caver2

2010-11-09T08:56:28Z

Hci:

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:ukazky-plugin.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:ukazky.png|1000px]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:

Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0]", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"[http://decibel.fi.muni.cz/download/papers/medek08.pdf Computation of tunnels in protein molecules using delaunay triangulation]". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

Caver2

2010-11-09T08:56:16Z

Hci:

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:ukazky-plugin.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:ukazky.png|800px]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:

Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0]", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"[http://decibel.fi.muni.cz/download/papers/medek08.pdf Computation of tunnels in protein molecules using delaunay triangulation]". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

File:Ukazky-plugin.png

2010-11-09T08:54:38Z

Hci:

Caver2

2010-11-09T08:54:07Z

Hci:

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:ukazky-plugin.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:ukazky.png]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:

Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0]", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"[http://decibel.fi.muni.cz/download/papers/medek08.pdf Computation of tunnels in protein molecules using delaunay triangulation]". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

Caver2

2010-11-09T08:53:50Z

Hci:

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:ukazky_plugin.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:ukazky.png]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:

Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0]", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"[http://decibel.fi.muni.cz/download/papers/medek08.pdf Computation of tunnels in protein molecules using delaunay triangulation]". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

File:Ukazky.png

2010-11-09T08:53:10Z

Hci:

File:Ukazky-plugin.PNG

2010-11-09T08:52:58Z

Hci:

Caver2

2010-11-09T08:46:03Z

Hci:

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:caver_plugin1.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:caver_plugin2.png]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:

Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0]", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"[http://decibel.fi.muni.cz/download/papers/medek08.pdf Computation of tunnels in protein molecules using delaunay triangulation]". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

Caver2

2010-11-09T08:45:46Z

Hci:

'''CAVER 2.0'''

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:caver_plugin1.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:caver_plugin2.png]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:

Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0]", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"[http://decibel.fi.muni.cz/download/papers/medek08.pdf Computation of tunnels in protein molecules using delaunay triangulation]". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

Caver2

2010-11-09T08:44:18Z

Hci:

'''CAVER 2.0'''

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:caver_plugin1.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:caver_plugin2.png]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:

Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0]", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"Computation of tunnels in protein molecules using delaunay triangulation". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

Caver2

2010-11-09T08:43:40Z

Hci:

'''CAVER 2.0'''

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:caver_plugin1.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

[[File:caver_plugin2.png]]

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

References:
Medek, Petr and Beneš, Petr and Kozlíková, Barbora and Chovancová, Eva and Pavelka, Antonín and Szabó, Tibor and Zamborský, Matúš and Andres, Filip and Klvaňa, Martin and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří. "CAVER 2.0", 2008.

Medek, Petr and Beneš, Petr and Sochor, Jiří,"Computation of tunnels in protein molecules using delaunay triangulation". Journal of WSCG. Volume 15(1-3), 2007, Pages: 107-114.

Caver2

2010-11-09T08:39:03Z

Hci:

Caver2

2010-11-09T08:37:31Z

Hci:

'''CAVER 2.0'''

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:caver_plugin1.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

Caver2

2010-11-09T08:37:14Z

Hci:

'''CAVER 2.0'''

[http://loschmidt.chemi.muni.cz/caver.html CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

[[File:pymol_plugin1.png]]

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

File:Caver plugin2.png

2010-11-09T08:35:45Z

Hci:

File:Caver plugin1.png

2010-11-09T08:35:29Z

Hci:

Caver2

2010-11-09T08:35:00Z

Hci:

Caver2

2010-11-09T08:12:24Z

Hci:

Caver2

2010-11-09T08:11:22Z

Hci:

Caver2

2010-11-09T08:10:09Z

Hci:

'''CAVER 2.0'''

[ http://loschmidt.chemi.muni.cz/caver CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

Caver2

2010-11-09T08:09:49Z

Hci:

'''CAVER 2.0'''
[ http://loschmidt.chemi.muni.cz/caver CAVER 2.0] is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

Caver

2010-11-09T08:08:07Z

Hci:

A new version, CAVER 2.0, was recently developed. For further information see [http://www.pymolwiki.org/index.php/CAVER_2.0 CAVER 2.0 PyMOLWiki page]

Previous CAVER 1.0 (no longer maintained) provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is important in drug design and molecular enzymology to understand binding of inhibitors to the receptors, substrate binding and product egress from the enzyme active sites. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc.

References:

Petřek M., Otyepka M., Banáš P., Košinová P., Koča J. and Damborský J., [http://loschmidt.chemi.muni.cz/peg/abstracts/bmcbioinf06.html CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities], BMC Bioinformatics 2006, 7: 316

Damborský J., Petřek M., Banáš P., Otyepka M., [http://loschmidt.chemi.muni.cz/peg/abstracts/btj07a.html Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles], Biotechnology Journal 2007, 2: 62-67

[[Image:Caver.png]]

[[Category:Surfaces and Voids|Caver]]
[[Category:Nucleic_Acids|Caver]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

Caver

2010-11-09T08:07:07Z

Hci:

A new version, CAVER 2.0, was recently developed. For further information see [http://www.pymolwiki.org/index.php/CAVER_2.0:CAVER 2.0 PyMOLWiki page]

Previous CAVER 1.0 (no longer maintained) provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is important in drug design and molecular enzymology to understand binding of inhibitors to the receptors, substrate binding and product egress from the enzyme active sites. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc.

References:

Petřek M., Otyepka M., Banáš P., Košinová P., Koča J. and Damborský J., [http://loschmidt.chemi.muni.cz/peg/abstracts/bmcbioinf06.html CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities], BMC Bioinformatics 2006, 7: 316

Damborský J., Petřek M., Banáš P., Otyepka M., [http://loschmidt.chemi.muni.cz/peg/abstracts/btj07a.html Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles], Biotechnology Journal 2007, 2: 62-67

[[Image:Caver.png]]

[[Category:Surfaces and Voids|Caver]]
[[Category:Nucleic_Acids|Caver]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

Caver

2010-11-09T08:05:56Z

Hci:

A new version, CAVER 2.0, was recently developed. For further information see [[http://www.pymolwiki.org/index.php/CAVER_2.0]]

Previous CAVER 1.0 (no longer maintained) provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is important in drug design and molecular enzymology to understand binding of inhibitors to the receptors, substrate binding and product egress from the enzyme active sites. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc.

References:

Petřek M., Otyepka M., Banáš P., Košinová P., Koča J. and Damborský J., [http://loschmidt.chemi.muni.cz/peg/abstracts/bmcbioinf06.html CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities], BMC Bioinformatics 2006, 7: 316

Damborský J., Petřek M., Banáš P., Otyepka M., [http://loschmidt.chemi.muni.cz/peg/abstracts/btj07a.html Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles], Biotechnology Journal 2007, 2: 62-67

[[Image:Caver.png]]

[[Category:Surfaces and Voids|Caver]]
[[Category:Nucleic_Acids|Caver]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

Caver

2010-11-09T08:00:44Z

Hci:

[[http://www.pymolwiki.org/index.php/CAVER_2.0]]

CAVER 1.0 provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is important in drug design and molecular enzymology to understand binding of inhibitors to the receptors, substrate binding and product egress from the enzyme active sites. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc.

References:

Petřek M., Otyepka M., Banáš P., Košinová P., Koča J. and Damborský J., [http://loschmidt.chemi.muni.cz/peg/abstracts/bmcbioinf06.html CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities], BMC Bioinformatics 2006, 7: 316

Damborský J., Petřek M., Banáš P., Otyepka M., [http://loschmidt.chemi.muni.cz/peg/abstracts/btj07a.html Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles], Biotechnology Journal 2007, 2: 62-67

[[Image:Caver.png]]

[[Category:Surfaces and Voids|Caver]]
[[Category:Nucleic_Acids|Caver]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

Caver2

2010-11-09T07:59:44Z

Hci: Created page with 'CAVER 2.0 CAVER 2.0 is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solv…'

CAVER 2.0

CAVER 2.0 is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

User:Hci

2010-11-09T07:52:17Z

Hci:

'''CAVER 2.0
'''

CAVER 2.0 is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

User:Hci

2010-11-09T07:50:59Z

Hci: Created page with ''''CAVER 2.0 ''' == Headline text == CAVER 2.0 is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried c…'

'''CAVER 2.0
'''
== Headline text ==

CAVER 2.0 is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.

CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL application, you can download the CAVER plugin for PyMOL. Then the standard functionality of PyMOL application for the subsequent exploration of computed channels can be used. The other possibility is to take advantage of our CAVER Viewer application, which has been designed exactly for the problem of detection and mainly for further exploration of channels. It includes the CAVER 2.0 algorithm for computation of channels in static molecule as well as in molecular dynamics. CAVER Viewer can be downloaded and installed as a standalone version or you can use the online version based on the Java Web Start technology.

Caver

2010-11-09T07:38:20Z

Hci:

CAVER 1.0 provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is important in drug design and molecular enzymology to understand binding of inhibitors to the receptors, substrate binding and product egress from the enzyme active sites. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc.

References:

Petřek M., Otyepka M., Banáš P., Košinová P., Koča J. and Damborský J., [http://loschmidt.chemi.muni.cz/peg/abstracts/bmcbioinf06.html CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities], BMC Bioinformatics 2006, 7: 316

Damborský J., Petřek M., Banáš P., Otyepka M., [http://loschmidt.chemi.muni.cz/peg/abstracts/btj07a.html Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles], Biotechnology Journal 2007, 2: 62-67

[[Image:Caver.png]]

[[Category:Surfaces and Voids|Caver]]
[[Category:Nucleic_Acids|Caver]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]