Design and Implementation of Navigation System for Protein Interaction Networks

Proteins may not only perform a few of molecular functions, but it may also have many interactions with other proteins to accomplish a biological process successfully in cell [1]. These interactions could be defined as PINs (Protein Interaction Network). In general, researchers may adopt the yeast two-hybrid system for identifying protein interaction and it should be managed in database systematically such as BIND, DIP, YPD, PIMdb, and etc. But it’s not easy for user to analyze and interpret complicated PINs directly. There are application system to support this problem such as Cytoscape [4], Osprey [5], Tulip, and etc. But, these systems aren’t able to retrieve PINs which include proteins that have specific function and biological process, and interact with others at particular position in cell. Also, most systems use FDP (Force-Directed Placement) [3] algorithm for visualization, but this algorithm is not suitable to layout PINs because they are consisted of many disconnected sub-networks.