ClusPro Server

ClusPro

Filtering, Clustering, and Ranking Protein-Protein Complexes


Application: Protein-Protein Docking Web Server
Ranking of receptor-ligand complexes using energy filtering and clustering

Click here for documentation, bugs and other information.

See our latest results at CAPRI

Check the status of your job

In order to allow as many users as possible to utilize ClusPro, we ask that researchers submit no more than 5 jobs per day!!!

Required Fields


Upload receptor pdb file*

OR enter receptor PDB code* for direct download from PDB database and desired chain IDs (leave blank to use all chains):

Upload ligand pdb file*

OR enter ligand PDB code* for direct download from PDB database and desired chain IDs (leave blank to use all chains):


*The pdb files that are entered will be modified to contain the polar hydrogens using CHARMm


Email address to send the results:

If you are at an academic institution, please use that email address instead of a general hotmail/yahoo/gmail account.
Thank you.

Advanced Options


Choose docking program to use from DOT, ZDOCK, or GRAMM.
**Note: GRAMM is not currently available for docking. The server can only process its output**


Upload your output file (must contain at least 2000 decoys)
**Note: The uploaded decoy file must correspond to the PDBs entered above**
**Note: The corresponding docking algorithm must be specified above**
**If the ZDOCK server was used for docking, please use the PDBs they supplied in their output**




Select the radius (in Angstroms) of which the clustering is performed
For smaller complexes, it is recommended to decrease the clustering radius


Select the number of electrostatic hits that you would like to cluster. The number of ACP hits clustered will be 2000-Elec


Select the number of structures you would like to receive in the output

Homo-Multimeric Docking


This option allows for the generation of decoys based upon docking two identical molecules together
and forming a multimer (the user must know how many how many subunits make up the multimer)

Select the number of identical monomers that constitute the multimer


Select the number of conformations you would like to retain in the initial docking step.


        

Please cite: S.R. Comeau,D.W. Gatchell, S. Vajda, C.J. Camacho. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics, 20, 45-50
and

S. R. Comeau, D.W. Gatchell, S. Vajda, C.J. Camacho. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research Vol 32, W96-99, as well as the references for the docking software used.

For Multimeric Docking, please also cite:

S.R. Comeau, C.J. Camacho. Predicting oligomeric assemblies: N-mers as a primer. J. Struct. Biol., 2005 Jun 150(3):233-44

Scripts

We have made scripts available for blocking certain residues from docking and for docking to specific residues. The user must pre-process their PDB files with these programs in order to block/attract certain regions. As a note, the blocking/attracting can only be done on the receptor PDB file, due to the nature of DOT. This feature is not compatible with ZDOCK.

block.pl
attract.pl


We have made a script available which generates 1 file per model in order to view ClusPro's output with ease.

split_models.pl

Please report technical problems and bugs to scomeau@tonka.bu.edu

For comments and licensing contact scomeau@tonka.bu.edu