Cavity programs: Difference between revisions

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This page lists programs that identify and offer visualization options for cavities in macromolecules. Broadly, the term "'''cavities'''" includes pockets, tunnels and channels.

*An '''entrance''' is an opening from the cavity to solvent at the surface of the macromolecule.

*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<ref name="damborsky3">PMID: 27957758</ref><ref name="kingsley">PMID: 25663659</ref><ref name="caverweb" />.

*A '''channel''' connects two entrances ~~from solvent at the macromolecular surface~~<ref name="caverweb" />.

*A '''channel''' connects two entrances<ref name="caverweb" />.

*Some cavities are buried with no entrances ~~from the surface~~ (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>.

*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>.

Nearly all proteins have irregular surfaces with 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<ref name="damborsky3" /><ref name="kingsley" />.

Cavity programs: Difference between revisions

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 This page lists programs that identify and offer visualization options for cavities in macromolecules. Broadly, the term "'''cavities'''" includes pockets, tunnels and channels.
+*An '''entrance''' is an opening from the cavity to solvent at the surface of the macromolecule.
 *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<ref name="damborsky3">PMID: 27957758</ref><ref name="kingsley">PMID: 25663659</ref><ref name="caverweb" />.
-*A '''channel''' connects two entrances from solvent at the macromolecular surface<ref name="caverweb" />.
+*A '''channel''' connects two entrances<ref name="caverweb" />.
-*Some cavities are buried with no entrances from the surface (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>.
+*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>.
 Nearly all proteins have irregular surfaces with 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<ref name="damborsky3" /><ref name="kingsley" />.