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If ATOM entry contains residues other than 20 amino acids (A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y). Then job may terminate abnormally with an error message "Receptor/Ligand Molecule is not in PDB format".

Receptor and Ligand File
Upload receptor and ligand file which were used to generate docking decoys. DO NOT interchange the receptor and ligand file.

Transformation Matrix
Docking search program outputs a file containing all the information for generation of docking orientations. Upload that file.

For example,
FTDock program outputs ftdock_global.dat,
ZDOCK program outputs zdock.out,
PatchDock program outputs output.txt,
GrammX program outputs output.res .

Please DO NOT upload any structure file as Transformation Matrix. In that case, the program will terminate without any warning/error message.

Format of Transformation Matrix
The server will generate the docking orientations from uploaded transformation matrix using uploaded receptor and ligand proteins. Thus, user is asked to select the correct file format of transformation matrix. Currently, PRUNE server supported file format are: FTDock, ZDOCK, PatchDock, and GrammX.

Upload only receptor and ligand files along with the transformation file required for generation of docking orientations. If there is need of any intermediate files (like .ms file in PatchDock), that will be generated by the server.

Personal Information
If you have provided email id then job submission and completion notification will be sent through email. Otherwise, you have to bookmark the status page which will appear immediately after job submission. The status page will show the job status information, and after successful completion of the job, will display result. All the jobs in this server are confidential.

Example run
The example files are at the example folder.
Step 1:
Upload receptor and ligand molecules used for generating docking decoys (Figure 1).

Figure 1

Upload the Transformation Matrix generated during docking search. We have used FTDock program module so, the default output file is ftdock_global.dat

The file format of transformation matrix is FTDock. Thus, FTDock option is selected under "Format of Transformation Matrix".

Enter your name and email id for communicating job related information.

Click on Submit button.

Figure 2

The server will show a brief summary of the proteins (Figure 2).

Press the button "PRUNE" to submit job at the linux cluster. The job submission notification, with the link of the status of the job, will be sent through email.

Step 2:
Contact area is the only parameter which is used for pruning docking decoys. Contact area is defined as the difference between the total accessible surface area (ASA) of the subunits and the complex. NACCESS program module is used for this purpose. NACCESS takes 2-3 seconds for computing ASA of a protein. Thus, the time requirement, for each job in PRUNE server, is the number of decoys multiplied by the time requirement of NACCESS for a complex.

The result page (Figure 3) will allow the user to download Receptor Molecule, Ligand Molecule and the Pruned Transformation Matrix. Receptor and ligand molecule is same as was uploaded. Pruned transformation matrix will contain the information of only pruned (a proper subset of all) decoys.

The option for scoring pruned decoys has been provided at the result page. The scoring method is an implementation of Mitra & Pal (2010). To score and rank the decoys press the button "Score PRUNEd Decoy". The scoring and ranking result page is same as PROBE result page.

Figure 3

Happy PRUNEing !!!