12.10 Pockets - Protein cavity detection

 

12.10.1 Introduction

Pockets is the graphic interface for fpocket, the well known software developed by Vincent Le Guilloux and Peter Schmidtke to detect protein cavities. This program uses an extremely optimized algorithm based on Voronoi tessellation that is very fast and allows to analyze large molecules waiting for a reasonable time.

The Pockets plug-in was developed with the intent to integrate fpocket into the VEGA ZZ enviroment making easier the use of this command-line oriented software. The possibility to identify protein cavities is very useful to perform blind docking studies when the binding site is unknown. Fpocket with its Pockets plug-in help you to scan the target protein to find the best pockets able to accommodate ligands which binding mode is not yet identified.

 

12.10.2 Usage

Before to start the pocket analysis, the protein to study must be loaded in the VEGA ZZ environment. After this operation, the Pockets main window can be shown selecting Calculate Pockets in VEGA ZZ main menu:

 

Pockets main window

 

 

In Fpocket parameters box, you can set all parameters to control the cavity search and for an exhaustive explanation, you must consult the fpocket manual. In Post processing box, it's possible to define the actions after the fpocket calculation: checking  Load spheres, the spheres, calculated by fpocket to fill the cavities, are automatically loaded in the 3D graphic window of VEGA ZZ and/or checking Show surface, starting from the spheres, the cavity surfaces are calculated and shown. In Color box, you can define the coloring methods of cavities: None (default color only), By cavity (each cavity has a different color) and By property (the surface is colored by polar (violet) and apolar (sand) properties).

Clicking Run button, the file requester is shown asking you the PDB file needed as input by fpocket and clicking Save button, the fpocket calculation starts. At the end, the results are automatically loaded in the table list of the plug-in window. The cavities are sorted by score and the meaning of each column is explained in the fpocket manual. If the cavitieas aren't already shown in the VEGA ZZ main window, it's possible to show them double clicking on each rows. Clicking the table by the right mouse button, the context menu is shown and the its features are summarized in the following table:

 

Menu Item Description
Open

Open the cavities previously calculated. You can select the *_out or the pockets directory. If the current workspace is empty, you can't show the surfaces double clicking on them.

Save as ... Save the surface table in Comma Separated Values (CSV) format or in Data Interchange Format (DIF).
Show Show the highlighted surface in the VEGA ZZ graphic environment.
Copy Copy the value under the mouse pointer to the clipboard.
Copy row Copy the row to the clipboard. The values are separated by space characters.
Copy all Copy the whole table to the clipboard in CSV format.
Send to Excel Send the all results to Microsoft Excel through the DDE connection.
Remove pockets Remove all pockets from the current VEGA ZZ view.

 

Some of these functions are replicated in the menu bar, as shown in the following table:

 

Menu Submenu Description
File Open Open the cavities previously calculated. You can select the *_out or the pockets directory. If the current workspace is empty, you can't show the surfaces double clicking on them.
Save as ... Save the surface table in Comma Separated Values (CSV) format or in Data Interchange Format (DIF).
Close Close the plug-in window.
Edit Calculate pockets Run fpocket to calculate the cavities. It's equivalent to press the Run button.
Copy row Copy the row to the clipboard. The values are separated by space characters.
Copy all Copy the whole table to the clipboard in CSV format.
Send to Excel Send the all results to Microsoft Excel through the DDE connection.
Remove pockets Remove all pockets from the current VEGA ZZ view.
Help Manual Show the plug-in manual.
About Show the copyright message.

 

Clicking the Default button, you can revert to default settings.

 

Notes:

All fpocket executables (dpocket, fpocket and tpocket) are included in the VEGA ZZ package and can be used as command-line programs.