Cavity programs

From Proteopedia

Revision as of 20:32, 15 December 2020 by Eric Martz (Talk | contribs)
Jump to: navigation, search

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 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 can identify and display pockets and cavities as isosurfaces. Examples are shown at Jmol/Cavities pockets and tunnels.

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

Retrieved from "http://52.214.119.220/wiki/index.php/Cavity_programs"
Personal tools