Protein-Protein Docking (PPD) takes two protein structures and computationally determines the structure of the protein-protein complex. The PPD pipeline integrates and automates this protein docking process employing DoD High Performance Computing (HPC) systems. The current genome sequencing effort and genome-wide protein structure determination make PPD a promising approach to structurally characterize protein-protein interactions on the genomic level.

The pipeline aims at integrating various state-of-the-art techniques of protein docking at different stages:

• Binding interface prediction and biochemical information filtering
• Fast Fourier Transform-based rigid-body docking of decoy prediction
• High-resolution docking incorporating protein flexibility
• Post-docking minimization and Molecular Dynamics simulation refinement
• Clustering and consensus scoring

Efficient approaches and optimized protocols will be developed based on standard benchmarks of known binding complexes and validated by various data sets, including the Critical Assessment of PRedicted Interactions (CAPRI).

Application of the pipeline, combined with the protein 3D structure prediction software suite (PSPP), is aimed at studies of large-scale protein-protein interaction (PPI) networks of biodefense-related organisms.