Cavity programs
From Proteopedia
(New page: This page lists programs that identify and offer visualization options for cavities in macromolecules. Broadly, the term "cavities" includes pockets, tunnels and channels. A pocket is a de...) |
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Nearly all proteins have shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a pocket can also be termed a tunnel accessing the catalytic site. | Nearly all proteins have shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a pocket can also be termed a tunnel accessing the catalytic site. | ||
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| + | Programs are listed alphabetically. | ||
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| + | ==Jmol== | ||
| + | [[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]]. | ||
Revision as of 20:21, 15 December 2020
This page lists programs that identify and offer visualization options for cavities in macromolecules. Broadly, the term "cavities" includes pockets, tunnels and channels. A pocket is a depression in the surface with one entrance. A tunnel connects two or more locations, and may or may not have entrances from the surface. Some cavities are buried with no entrances from the surface (example: 3drf).
Nearly all proteins have shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. 1vot). Such a pocket can also be termed a tunnel accessing the catalytic site.
Programs are listed alphabetically.
Jmol
Jmol can identify and display pockets and cavities as isosurfaces. Examples are shown at Jmol/Cavities pockets and tunnels.
