Cavity programs: Difference between revisions

*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="moleonline" /><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" />.

The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. Programs are listed alphabetically.  

[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown.

[[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 is updated often, most recently November 19, 2020.

PACUPP, '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). 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 [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program.

PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a spreadsheet-ready text file. Learning the PACUPP commands is much easier than learning Jmol commands.