EBMDock: Neural Probabilistic Protein-Protein Docking via a Differentiable Energy Model

Published: 16 Jan 2024, Last Modified: 21 Apr 2024ICLR 2024 posterEveryoneRevisionsBibTeX
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Keywords: protein-protein docking, energy-based model, geometric deep learning, energy-function
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Abstract: Protein complex formation, a pivotal challenge in contemporary biology, has recently gained interest from the machine learning community, particularly concerning protein-ligand docking tasks. In this paper, we delve into the equally crucial but comparatively under-investigated domain of protein-protein docking. Specifically, we propose a geometric deep learning framework, termed EBMDock, which employs statistical potential as its energy function. This approach produces a probability distribution over docking poses, such that the identified docking pose aligns with a minimum point in the energy landscape. We employ a differential algorithm grounded in Langevin dynamics to efficiently sample from the docking pose distribution. Additionally, we incorporate energy-based training using contrastive divergence, enhancing both performance and stability. Empirical results demonstrate that our approach achieves superior performance on two benchmark datasets DIPS and DB5.5. Furthermore, the results suggest EBMDock can serve as an orthogonal enhancement to existing methods.
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Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)
Submission Number: 3084