This page is dedicated to describe in detail how to use and run fpocket server. For several reasons, two servers are available to run hpocket:

• Default server
• Advanced server (Mobyle)

In this page, you will find detailed documentation on how to run fpocket for both servers (input & output).

There are two (very simple) ways to run fpocket, valid on both servers:

• Run fpocket for a single potein
• Run fpocket for a set of proteins

The way you have to enter the data is very simple, though slightly different for each server, and is described bellow.

Default server

Running a fpocket job

1. For a single potein, you can either browse (2) your local hard drive to provide a PDB file, or directly paste (1) your PDB file in the text area.
2. For a set of proteins, it is exactly the same as previously described, but in a different field shown below. Note that, the server allows you to type directly a list of PDB ids formated in one single column (one PDB id per line).
    
   
3. Optionally, enter your email (3) to be notified when your job will be finished.
4. Once your data has been entered properly, you will have to enter the word shown in the captcha image (4). This is to avoid automatic programs to do nasty stuff with our server.
5. You can now run fpocket by clicking on the Submit button (GO!). Clicking on the clear button will clear all input data you entered

Alternatively, you can test the server, using inhouse demonstration data. To do so, just check the Demo checkbox shown in the picture bellow, and go to step 3 (any input data will be discarded then).

Note that you can give a name to your job using the following text field. The default name contains the service name plus the current date and time.

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Intermediate page (job status)

Once you have submitted your data, a new job will be created. You will be redirected to an intermediate page. From there, you just have to wait the end of your job, or bookmark the result page using the adress given in this page. Then, when your job will be finished, you will have a new intermediate page, from where you will have to click on the provided link to obtain the results page described in the output results section.

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Advanced server (Mobyle)

Running a fpocket job

To run fpocket using Mobyle, you need to provide the same input types as described for the default server. The only difference is the interface, and that you have the possibility to retrieve PDBs directly from the Protein Data Bank.

Here is a short description of the mobyle interface:

1. For a single potein, use the first form labeled Query PDB (PDB), shown in the snapshots bellow. You have 3 possibilities to enter your data, each of these being selected by clicking on the corresponding radio button:
   1. Copy/paste (1): Simply copy and paste your PDB data in the text area.
   2. Database (2): Select your database using the combo box (a), and enter a valid PDB 4 letter code (b).
   3. Local file (b): Select a local file stored on your computer.
   
    
2. For multiple proteins, use the second form labeled Query multiple PDB. Usage is exactely the same as described for the single PDB form. Note that, once again, the server allows you to enter a list of PDB ids formated in one column (one id per line). Moreover, if you click the DB radio button, choose PDB, type your PDB id and then click the add button, Mobyle will add your query PDB file at the end of the previous one. This creates a multiPDB file on-the-fly.
3. You can now run fpocket by clicking on the Run button (GO!). Clicking on the Reset button will clear all input data you entered
4. The first time you will run fpocket, you will have to enter a security string. Don't worry, you only have to do this the first time you run fpocket.

You can also test the server by using demonstration data. To do so, just check the Demo checkbox shown in the picture bellow, and go to set 3 directly (any input data will be discarded then).

Note that you can also give a name to your job using the following text field.

Intermediate page (job status)

Once you have submitted your data, a new job will be created, and you will be redirected to this new job tab page as shown bellow. From here, you just have to wait for results to appear.

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We use the same output page to display results of fpocket job for both server. Before describing it, we just describe for both servers, how to reach this page. Don't worry it's really easy.

Getting to the results page

Default server

Just follow the input tutorial, where we describe all intermediates pages from which you will be able to reach the results final page.

Advanced server (Mobyle)

In mobyle, once your job will be finished, you will be redirected to the mobyle results page. This results page is shown in the snapshot on the right. You will notice that it is not yet really clear; the results page is actually contained in the "Detected pocket alpha spheres (fPocket HTML)" labeled scroll pane. Anyway, to reach the results page described in the next section, just click on the Full screen view button (1)

You also have the possibility to bookmark the result page using the Bookmark button (2) (enter the bookmark name in the field on left)

Main program output results are provided both in the final results page and in the mobyle interface. This redundancy is comfortable to (i) analyse your results in a specific and integrated web page and (ii) to directly use the mobyle pipelining feature for further analysis.

Results page description

The results can be roughly divided in 3 sections: Output files, Snapshots and Visualisation .

Output files

Several fpocket output files are provided and described bellow. You can download all of them.

• Pymol visualisation script (1): it consists of a pymol visualisation script that allows you to view fpocket results using pymol. The .pml is the actual script, and the .sh should be used to run the script. Note that this script cannot be used without fpocket output pdb files. A tar archive is therefore provided that include all files (pymol script, sh launcher & fpocket output pdb)
• VMD visualisation script (2): same as Pymol, but for VMD.
• Fpocket main output file (3), containing the input PDB and all alpha spheres as dummy carbon HETATM.
• Alpha spheres only (4) representing each pockets, as a PQR file.

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Snapshots

A set of PDB snapshots are provided (generated by Pymol), showing predicted pockets as surfaces of each pockets atoms. These snapshots might disappear soon when the openAstex viewer will be released.

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Visualisation

If you don't like VMD or Pymol, or if you just want to have a quick view of fpocket results without doing anything, you can use either Jmol or OpenAstex interactive applets at the bottom of the page. The fpocket output PDB file automatically loaded in the choosen viewer on the right, (1), with alpha spheres shown in CPK mode (gray = apolar alpha spheres, red = polar alpha spheres, see hint 3 on the right).

On the right, you have a set of graphic components to facilitate the viewing. A small set of options (2) allows you to perform various changes to the whole system representation (display protein as cartoon, reset view...). We will progressively add more of these utilities.

All pockets are listed on the bottom left of the visualisation part (3) (positon = rank). You also have various display possibilities depending on the viewer, and for both of them, you can dowload the pocket as PDB file (all atoms contacted by alpha spheres) or PQR file (all alpha spheres).

Remember that for both viewers, you can access the display popup menu by right clicking on the view.