Protein Multimer Structure Prediction via Prompt Learning

Published: 16 Jan 2024, Last Modified: 21 Apr 2024ICLR 2024 posterEveryoneRevisionsBibTeX
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Keywords: docking path prediction, protein complex structure, prompt learning
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TL;DR: A pre-training and prompt tuning approach for predicting complex 3D structures in a step-wise assembly fashion.
Abstract: Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction (MSP) can be well handled in a step-wise assembly fashion using provided dimer structures and predicted protein-protein interactions (PPIs). However, due to the biological gap in the formation of dimers and larger multimers, directly applying PPI prediction techniques can often cause a poor generalization to the MSP task. To address this challenge, we aim to extend the PPI knowledge to multimers of different scales (i.e., chain numbers). Specifically, we propose PromptMSP, a pre-training and Prompt tuning framework for Multimer Structure Prediction. First, we tailor the source and target tasks for effective PPI knowledge learning and efficient inference, respectively. We design PPI-inspired prompt learning to narrow the gaps of two task formats and generalize the PPI knowledge to multimers of different scales. We provide a meta-learning strategy to learn a reliable initialization of the prompt model, enabling our prompting framework to effectively adapt to limited data for large-scale multimers. Empirically, we achieve both significant accuracy (RMSD and TM-Score) and efficiency improvements compared to advanced MSP models.
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Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)
Submission Number: 2316