Pockets / Cavities

Pockets and cavities are currently identified in STING using two different algorithms:
Pocket which is part of the package ProShape and NanoShaper. The NanoShaper is a new addition to STING suite and an extremely flexible tool, created with the specific aim of calculating the Molecular Surface (MS) of atomistic structures according to different possible definitions, namely the traditional Connolly Solvent Excluded Surface (SES), the Skin surface and the Blobby Gaussian surface.

The JPD interface presents information about pockets/cavities for each isolated chain and for the entire structure. Regarding the adopted color code, red boxes indicate pockets whereas the yellow ones indicate cavities.

Placing the cursor above this element: pop-up area will show the used software tool (ProShape or NanoShaper), the position (sequence number and AA three letter code) for selected amino acid and the number of Pocket/Cavity identified and to which a selected amino acid belongs.
Left mouse click: no action
Right mouse click: on any of the "Pocket/Cavity" boxes will generate a menu with a set of possible actions:

ProShape

NanoShaper

A) By pressing "STING Pocket/Cavity" (Complex or Isolation), the user is able to select which pockets/cavities for the selected residue will be displayed on the Jmol window. The user can also display simultaneously all the pocket/cavities for the whole protein.



B) By pressing "Pocket/Cavity Atom List" (Complex or Isolation) option, the user can select for which pocket/cavity the atoms should be listed on a HTML table.




C) Finally the option "STING Selected Pocket/Cavity from this Protein" (Complex or Isolation) is an alternative way for selecting pockets/cavities to be displayed on the Jmol window.