IV-KAPhE is a multi-label kinase-phosphosite assignment method that nests a multi-label model of in vitro assignment in a model of in vivo functional association.

Naïve Bayes+ consists of sub-models for each kinase, trained from kinase-specific, high-throughput in vitro kinase-substrate relationships. These sub-models together comprise a final, multi-label Naïve Bayes model. IV-KAPhE is a monolithic, multi-kinase Random Forest model trained from all literature-derived kinase-substrate annotations and random pairs as negative cases.