评估数据分区策略,准确预测突变蛋白质中蛋白质 - 配体结合的自由能量变化
Liangxu Xie1, Guoming Bao1, Dawei Zhang1
1Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China.
Computational and structural biotechnology journal
|October 31, 2025
概括
精确预测蛋白质 - 配体结合能量,对于药物设计至关重要,是通过一个新的查询对对学习框架改进. 该方法利用已知状态来增强未知状态的预测,克服机器学习模型中随机或基于UniProt的数据分割的局限性.
科学领域:
- 计算化学是一种计算化学.
- 结构生物学是结构生物学.
- 药物发现 药物发现
背景情况:
- 准确预测蛋白质 - 配体结合的自由能量对于药物设计和理解耐药性至关重要.
- 机器学习 (ML) 和深度学习 (DL) 模型经常面临由于数据集分区策略的泛化挑战.
- 随机分区可能会导致性能估计膨胀,而基于UniProt的分区会损害预测准确性.
研究的目的:
- 在MdrDB数据库上使用随机和基于UniProt的数据分区来评估六个ML/DL模型的性能.
- 开发一个新的框架,以提高ML / DL模型的概括性和准确性,以预测蛋白质-配体结合的自由能量,特别是蛋白质突变.
- 解决现有的数据分区策略在评估模型性能方面的局限性.
主要方法:
- 在MdrDB数据库上评估了六种不同的ML/DL模型.
- 用ESM-2蛋白质大语言模型嵌入蛋白质序列,整合野生类型和突变特征.
- 提出了一个查询对式学习框架,使用已知的状态作为预测未知的查询状态的点.
主要成果:
- 在随机分区下,所有评估的模型都显示出高的预测相关性 (Pearson系数高达0.70),但在基于UniProt的分区下,性能显著下降.
- 拟议的查询定双向学习框架在三个验证系统中展示了增强的预测准确性.
- 即使在查询 anchor框架中的少量参考数据也显著提高了预测准确性.
结论:
- 数据集分区策略的选择对评估ML/DL模型在预测蛋白质 - 配体结合的自由能量方面的表现产生了关键影响.
- 查询对式学习框架提供了一个强大的方法,通过有效利用已知的状态来提高预测准确性.
- 这种方法有望在药物设计和解释耐药性机制方面进行更可靠的预测.
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