[Proteopedia] New tool to locate and visualize pockets, cavities and tunnels

[Eric Martz]

A new, free, open-source program is available: PACUPP, Pockets And 
Cavities Using Pseudoatoms in Proteins.

You can see sample results at

http://proteopedia.org/w/PACUPP:_Pockets_And_Cavities_Using_Pseudoatoms_in_Proteins

There are demonstrations in YouTube and a slideshow. You can find these 
and download the program at http://molviz.org/pacupp

Examples shown include:

  * Coronoavirus SARS-CoV-2 spike protein cavity that is a potential
    drug target
  * Ribosome nascent peptide exit channel
  * Proteasome
  * HIV protease (detailed demonstration of PACUPP commands)
  * Acetylcholinesterase catalytic pocket with inhibitor
  * DNA, major and minor grooves
  * Orthogonal tunnels accessing the heme in protoglobin
  * Oligopeptide-binding protein A with an octapeptide in a buried
    cavity (detailed demonstration of PACUPP commands)

-Eric

Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his)
U Mass, Amherst -- Martz.MolviZ.Org <http://martz.molviz.org/>
Guided Exploration of Macromolecules: FirstGlance.Jmol.Org 
<http://firstglance.jmol.org/>
Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.org/>
Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.molviz.org/>
Education: Biochem in 3D at MolviZ.Org <http://molviz.org/>
Find Functional Patches in Proteins: ConSurf.tau.ac.il
Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.molviz.org/>
Interactive Molecules in Architectural Spaces: MolecularPlayground.Org 
<http://molecularplayground.org/>
Workshops: Workshops.MolviZ.Org <http://workshops.molviz.org/>
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