Cavity programs

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[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands.
[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands.
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Jmol has an extensive command language that provides great flexibility in visualizing cavities.
The Jmol Java standalone application is downloadable from [http://jmol.org jmol.org]. It is also available as JSmol, a Javascript implementation used in most pages in Proteopedia.
The Jmol Java standalone application is downloadable from [http://jmol.org jmol.org]. It is also available as JSmol, a Javascript implementation used in most pages in Proteopedia.

Revision as of 21:03, 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[1][2]. Some cavities are buried with no entrances from the surface (example: 3drf).

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[1][2].

Programs are listed alphabetically.

Jmol

Jmol:
Interior (buried) cavities in the SARS-CoV-2 spike protein rendered as isosurfaces by Jmol using a cavity probe radius of 2.6 Å and a surface smoothing probe radius of 10 Å. The membrane-proximal cavity (bottom) is a potential target for drugs to prevent membrane fusion, and thus prevent infection.

Jmol can identify and display pockets and cavities as isosurfaces. Examples are shown at Jmol/Cavities pockets and tunnels, where you will also find explanations of the interior cavity and pocket commands.

Jmol has an extensive command language that provides great flexibility in visualizing cavities.

The Jmol Java standalone application is downloadable from jmol.org. It is also available as JSmol, a Javascript implementation used in most pages in Proteopedia.

PACUPP

PACUPP, Pockets And Cavities Using Pseudoatoms in Proteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"). An example is presented in some detail at PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [molviz.org/pacupp], where you can also download the program.

References

  1. ↑ 1.0 1.1 Marques SM, Daniel L, Buryska T, Prokop Z, Brezovsky J, Damborsky J. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Med Res Rev. 2017 Sep;37(5):1095-1139. doi: 10.1002/med.21430. Epub 2016 Dec 13. PMID:27957758 doi:http://dx.doi.org/10.1002/med.21430
  2. ↑ 2.0 2.1 Kingsley LJ, Lill MA. Substrate tunnels in enzymes: structure-function relationships and computational methodology. Proteins. 2015 Apr;83(4):599-611. doi: 10.1002/prot.24772. Epub 2015 Feb 28. PMID:25663659 doi:http://dx.doi.org/10.1002/prot.24772

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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