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Workshop: Machine Learning in Structural Biology Workshop

Contrasting drugs from decoys

Samuel Sledzieski · Rohit Singh · Lenore J Cowen · Bonnie Berger


Protein language models (PLMs) have recently been proposed to advance drug-target interaction (DTI) prediction, and have shown state-of-the-art performance on several standard benchmarks. However, a remaining challenge for all DTI prediction models (including PLM-based ones) is distinguishing true drugs from highly-similar decoys. Leveraging techniques from self-supervised contrastive learning, we introduce a second-generation PLM-based DTI model trained on triplets of proteins, drugs, and decoys (small drug-like molecules that do not bind to the protein). We show that our approach, CON-Plex, improves specificity while maintaining high prediction accuracy and generalizability to new drug classes. CON-Plex maps proteins and drugs to a shared latent space which can be interpreted to identify mutually-compatible classes of proteins and drugs. Data and code are available at

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