Methods PaperPRASA: An integrated web server that analyzes protein interaction types

This work presents the Protein Association Analyzer (PRASA) (http://zoro.ee.ncku.edu.tw/prasa/) that predicts protein interactions as well as interaction types. Protein interactions are essential to most biological functions. The existence of diverse interaction types, such as physically contacted or functionally related interactions, makes protein interactions complex. Different interaction types are distinct and should not be confused. However, most existing tools focus on a specific interaction type or mix different interaction types. This work collected 7234058 associations with experimentally verified interaction types from five databases and compiled individual probabilistic models for different interaction types. The PRASA result page shows predicted associations and their related references by interaction type. Experimental results demonstrate the performance difference when distinguishing between different interaction types. The PRASA provides a centralized and organized platform for easy browsing, downloading and comparing of interaction types, which helps reveal insights into the complex roles that proteins play in organisms.

► The Protein Association Analyzer (PRASA) predicts protein interactions with types. ► Available at http://prasa.ee.ncku.edu.tw/ and http://prasa.csbb.ntu.edu.tw/ ► Accommodates three interaction types: physical, genetic and pathway interactions ► de novo predictor, which requires only protein primary sequences ► Evaluated on human and yeast and achieved good performance