An Integrated Docking Pipeline for the Prediction of Large-Scale Protein-Protein Interactions
ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD
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Knowledge of the three-dimensional 3D structures of protein complexes provides a fundamental understanding of biological systems, as well as novel insights for antimicrobial drug and vaccine design. Protein-protein docking is used to predict the 3D structures of protein complexes from their components in silico. In this study, we developed a protein-protein docking pipeline PPDP that integrates a variety of state-of-the-art protein docking and structure prediction techniques, providing a systematic platform to predict large-scale protein-protein interactions PPIs. The PPDP is deployed on high performance computing HPC clusters, thus enabling Department of Defense scientists to harness HPC resources to investigate the PPIs of biowarfare agents for the development of countermeasures. We applied the PPDP to investigate the binding interactions of Yersinia effector proteins with their chaperone and the underlying specificity of chaperoneeffector interactions.