Protease target prediction via matrix factorization

Abstract

MotivationProtein cleavage is an important cellular event, involved in a myriad of processes, from apoptosis to immune response. Bioinformatics provides in silico tools, such as machine learning-based models, to guide target discovery. State-of-the-art models have a scope limited to specific protease families (such as Caspases), and do not explicitly include biological or medical knowledge (such as the hierarchical protein domain similarity, or gene-gene interactions). To fill this gap, we present a novel approach for protease target prediction based on data integration.\n\nResultsBy representing protease-protein target information in the form of relational matrices, we design a model that: (a) is general, i.e., not limited to a single protease family; and (b) leverages on the available knowledge, managing extremely sparse data from heterogeneous data sources, including primary sequence, pathways, domains, and interactions from nine databases. When compared to other algorithms on test data, our approach provides a better performance even for models specifically focusing on a single protease family.\n\nAvailabilityhttps://gitlab.com/smarini/MaDDA/ (Matlab code and utilized data.)\n\nContactsmarini@med.umich.edu, or takutsu@kuicr.kyoto-u.ac.jp