DOCK/PIE(RR): Protein Docking Server

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

Protein-protein docking algorithm based on residue contact potential learned using SVM-style framework to minimize false positive rates and FFT based approximations of OPLS vdw energy and residue contact score.

Refinement is performed using interface side chain remodeling and energy minimization. Refined models are reranked using a combination of residue and atomic potentials.

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.



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! Server for small molecule docking coming up!

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).