|DOCK/PIERR model (yellow) superposed with crystal structure of complex 3asy (red)|
The DOCK/PIERR algorithm is a rigid protein-protein docking algorithm that calculates the structure of a complex given the PDB structures of the unbound chains. Consider using our server here.
A brief description of the algorithm is given below.
Surfaces of the input proteins are calculated using MSMS and an exhaustive FFT-based grid search is performed for each complex. The scoring function in the FFT search is based on a residue contact potential learnt using SVM-style framework to minimize false positive rates, along with an FFT-based approximation of OPLS van der waals energy.
The top scoring 524,288 FFT-based transformations for each complex are stored and clustered in rigid body space. Subsequently, the top scoring cluster centers are filtered for clashes, and clustered again using interface RMSD.
Refinement is performed on the top 1000 models from the previous step of rigid docking. First, side chains are reconstructed using SCWRL4 for interface residues. This is followed by a short in-vacuum energy minimization using OPLS force field in MOIL MD package. Refined models are reranked using a combination of residue and atomic potentials. The server uses the potential C3 mentioned in the Proteins (2013) paper.