Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling

• URL: http://arxiv.org/abs/2306.03117v3
• Date: Mon, 11 Mar 2024 19:54:30 GMT
• Title: Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling
• Authors: Jiarui Lu, Bozitao Zhong, Zuobai Zhang, Jian Tang
• Abstract summary: The dynamic nature of proteins is crucial for determining their biological functions and properties. Existing learning-based approaches perform direct sampling yet heavily rely on target-specific simulation data for training. We propose Str2Str, a novel structure-to-structure translation framework capable of zero-shot conformation sampling.
• Score: 23.74897713386661
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena. By utilizing empirically derived force fields, MC or MD simulations explore the conformational space through numerically evolving the system via Markov chain or Newtonian mechanics. However, the high-energy barrier of the force fields can hamper the exploration of both methods by the rare event, resulting in inadequately sampled ensemble without exhaustive running. Existing learning-based approaches perform direct sampling yet heavily rely on target-specific simulation data for training, which suffers from high data acquisition cost and poor generalizability. Inspired by simulated annealing, we propose Str2Str, a novel structure-to-structure translation framework capable of zero-shot conformation sampling with roto-translation equivariant property. Our method leverages an amortized denoising score matching objective trained on general crystal structures and has no reliance on simulation data during both training and inference. Experimental results across several benchmarking protein systems demonstrate that Str2Str outperforms previous state-of-the-art generative structure prediction models and can be orders of magnitude faster compared to long MD simulations. Our open-source implementation is available at https://github.com/lujiarui/Str2Str

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