FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation

• URL: http://arxiv.org/abs/2311.02326v1
• Date: Sat, 4 Nov 2023 04:57:13 GMT
• Title: FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation
• Authors: Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Ozlem Ozmen Garibay
• Abstract summary: Drug-Target Interaction (DTI) prediction is vital for drug discovery, yet challenges persist in achieving model interpretability and optimizing performance. We propose a novel transformer-based model, FragXsiteDTI, that aims to address these challenges in DTI prediction. FragXsiteDTI is the first DTI model to simultaneously leverage drug molecule fragments and protein pockets.
• Score: 0.09236074230806578
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Drug-Target Interaction (DTI) prediction is vital for drug discovery, yet challenges persist in achieving model interpretability and optimizing performance. We propose a novel transformer-based model, FragXsiteDTI, that aims to address these challenges in DTI prediction. Notably, FragXsiteDTI is the first DTI model to simultaneously leverage drug molecule fragments and protein pockets. Our information-rich representations for both proteins and drugs offer a detailed perspective on their interaction. Inspired by the Perceiver IO framework, our model features a learnable latent array, initially interacting with protein binding site embeddings using cross-attention and later refined through self-attention and used as a query to the drug fragments in the drug's cross-attention transformer block. This learnable query array serves as a mediator and enables seamless information translation, preserving critical nuances in drug-protein interactions. Our computational results on three benchmarking datasets demonstrate the superior predictive power of our model over several state-of-the-art models. We also show the interpretability of our model in terms of the critical components of both target proteins and drug molecules within drug-target pairs.

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