We propose a computational screening system of protein-protein interactions (PPIs) using protein tertiary structure data. Our system combines all-to-all protein docking and clustering to find interacting protein pairs. We tuned our prediction system using a subset of general protein docking benchmark data by applying various parameters and clustering algorithms. This method was also applied to a biological pathway estimation problem to show its use in network level analysis. The proposed approach to computational PPI detection is a promising methodology for mediating between structural studies and systems biology by utilizing cumulative protein structure data for pathway analysis.
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