arXiv:2410.15592q-bio.BMcs.CL2024-10被引 3

用深度学习区分蛋白结构是实验测得还是预测的,提升可靠性判断

CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin Evaluation

  • 基于结构敏感的监督学习,识别蛋白结构来源
  • 在四类结构上实现高精度溯源,准确率显著优于传统方法
  • 适合生物学家评估结构可信度,辅助功能研究与数据筛选

蛋白质结构对理解其功能和相互作用至关重要。当前许多蛋白结构预测方法正在丰富结构数据库。区分结构来源对于辨别实验解析与计算预测结构、评估预测方法可靠性以及指导下游生物学研究具有重要意义。基于结构预测的研究成果,我们开发了结构敏感的监督深度学习模型——晶体与预测结构评估器(CPE-Pro),用于蛋白结构的表征与来源判别。CPE-Pro 能够学习蛋白的结构信息并捕捉结构间差异,实现对四类结构的精准溯源,未来可拓展至更多类别。同时,我们利用 Foldseek 将蛋白结构编码为“结构序列”,并训练了一个蛋白结构序列语言模型(SSLM)。初步实验表明,相较于大规模基于氨基酸序列预训练的语言模型,‘结构序列’使语言模型能学习更丰富的蛋白特征,从而增强和优化结构表征。相关代码、模型权重及资料已公开于 https://github.com/GouWenrui/CPE-Pro-main.git。

原文摘要 · Abstract (English)

Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for distinguishing between experimentally resolved and computationally predicted structures, evaluating the reliability of prediction methods, and guiding downstream biological studies. Building on works in structure prediction, We developed a structure-sensitive supervised deep learning model, Crystal vs Predicted Evaluator for Protein Structure (CPE-Pro), to represent and discriminate the origin of protein structures. CPE-Pro learns the structural information of proteins and captures inter-structural differences to achieve accurate traceability on four data classes, and is expected to be extended to more. Simultaneously, we utilized Foldseek to encode protein structures into "structure-sequences" and trained a protein Structural Sequence Language Model, SSLM. Preliminary experiments demonstrated that, compared to large-scale protein language models pre-trained on vast amounts of amino acid sequences, the "structure-sequence" enables the language model to learn more informative protein features, enhancing and optimizing structural representations. We have provided the code, model weights, and all related materials on https://github.com/GouWenrui/CPE-Pro-main.git.

蛋白结构深度学习结构溯源语言模型

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