物理学报2023，Vol.72Issue(24)：290-298,9.DOI:10.7498/aps.72.20231060
使用中间层受监督的自编码器探索蛋白质的构象空间
Exploring proten's conformational space by using encoding layer supervised auto-encoder
摘要
Abstract
Protein function is related to its structure and dynamic change.Molecular dynamics simulation is an important tool for studying protein dynamics by exploring its conformational space,however,conformational sampling is a nontrivial issue,because of the risk of missing key details during sampling.In recent years,deep learning methods,such as auto-encoder,can couple with MD to explore conformational space of protein.After being trained with the MD trajectories,auto-encoder can generate new conformations quickly by inputting random numbers in low dimension space.However,some problems still exist,such as requirements for the quality of the training set,the limitation of explorable area and the undefined sampling direction.In this work,we build a supervised auto-encoder,in which some reaction coordinates are used to guide conformational exploration along certain directions.We also try to expand the explorable area by training through the data generated by the model.Two multi-domain proteins,bacteriophage T4 lysozyme and adenylate kinase,are used to illustrate the method.In the case of the training set consisting of only under-sampled simulated trajectories,the supervised auto-encoder can still explore along the given reaction coordinates.The explored conformational space can cover all the experimental structures of the proteins and be extended to regions far from the training sets.Having been verified by molecular dynamics and secondary structure calculations,most of the conformations explored are found to be plausible.The supervised auto-encoder provides a way to efficiently expand the conformational space of a protein with limited computational resources,although some suitable reaction coordinates are required.By integrating appropriate reaction coordinates or experimental data,the supervised auto-encoder may serve as an efficient tool for exploring conformational space of proteins.关键词
蛋白质构象空间/分子动力学模拟/机器学习/自编码器Key words
protein conformational space/molecular dynamics simulation/machine learning/auto-encoder引用本文复制引用
陈光临,张志勇..使用中间层受监督的自编码器探索蛋白质的构象空间[J].物理学报,2023,72(24):290-298,9.基金项目
国家重点研发计划(批准号:2021YFA1301504)、国家自然科学基金(批准号:91953101)和中国科学院战略性先导科技专项(B类)(批准号:XDB37040202)资助的课题.Project supported by the National Key Research and Development Program of China(Grant No.2021YFA1301504),the National Natural Science Foundation of China(Grant No.91953101),and the Strategic Priority Research Program(B)of the Chinese Academy of Sciences(Grant No.XDB37040202). （批准号:2021YFA1301504）
