DOCK/PIERR: Protein Docking Server
DOCK/PIERR model (light green) superposed with crystal structure of complex 3rd6 (dark green)

Important: Jobs can no longer be submitted to the server. The content of this page is here for historical purposes.

Protein-protein docking algorithm based on residue contact potential PIE and atomic potential PISA.

The server uses SCWRL4 , released by the Dunbrack Lab for side chain remodeling.

MOIL, MD package developed in our lab is used for energy minimization.

For detailed instructions on how to use the server, including common mistakes in job submission, please refer to our article on DOCK/PIERR server referenced below.


Please upload the files in PDB format: (one model if NMR structure)

Note: Please make sure that the receptor and ligand PDBs have different chain names.

Also, please make sure you are submitting two protein chains and not small molecule ligands!

Protein 1 (larger protein - Receptor)
Protein 2 (smaller protein - Ligand)
Email address (used to send your docking results!)

References:

1) D V S Ravikant and Ron Elber, "PIE - Efficient filters and coarse grained potentials for unbound protein-protein docking", Proteins,78, 400-419 (2010).

2) D V S Ravikant and Ron Elber, "Energy design for protein-protein interactions", Journal of Chemical Physics, 135, 065102 (2011).

3) Shruthi Viswanath, D V S Ravikant and Ron Elber, "Improving ranking of models for protein complexes using side chain remodeling and atomic potentials", Proteins, 81, 592-606 (2013).

4) Shruthi Viswanath, D V S Ravikant and Ron Elber, "DOCK/PIERR : web server for structure prediction of protein-protein complexes", Methods in Molecular Biology, 1137:199-207 (2014).