DARKIN: A zero-shot benchmark for phosphosite-dark kinase association using protein language models

Abstract

MotivationProtein Language Models (pLMs) have emerged as powerful tools for capturing the intricate information encoded in protein sequences, facilitating various downstream protein prediction tasks. With numerous pLMs available, there is a critical need for diverse benchmarks to systematically evaluate their performance across biologically relevant tasks. Here, we introduce DARKIN, a zero-shot classification benchmark designed to assign phosphosites to understudied kinases, termed dark kinases. Kinases, which catalyze phosphorylation, are central to cellular signaling pathways. While phosphoproteomics enables the large-scale identification of phosphosites, determining the cognate kinase responsible for the phosphorylation event remains an experimental challenge. ResultsIn DARKIN, we prepared training, validation, and test folds that respect the zero-shot nature of this classification problem, incorporating stratification based on kinase groups and sequence similarity. We evaluated multiple pLMs using two zero-shot classifiers: a novel, training-free k-NN-based method, and a bilinear classifier. Our findings indicate that ESM, ProtT5-XL, and SaProt exhibit superior performance on this task. DARKIN provides a challenging benchmark for assessing pLM efficacy and fosters deeper exploration of under-characterized (dark) kinases by offering a biologically relevant test bed. ImplementationThe DARKIN benchmark data and the scripts for generating additional splits are publicly available at: https://github.com/tastanlab/darkin Contactotastan@sabanciuniv.edu Supplementary informationSupplementary data are available at Bioinformatics online.