中国科学院过程工程研究所多相复杂系统国家重点实验室，北京 100190
收稿日期:2018-06-28修回日期:2018-09-04出版日期:2018-12-22发布日期:2018-12-19通讯作者:任瑛基金资助:国家自然科学基金;中国科学院过程工程研究所介科学研究中心项目;中国科学院过程工程研究所多相复杂系统国家重点实验室开放课题Frontiers of molecular dynamics simulations of protein systems-reexamine from the mesoscience perspective
Ying REN*, Ji XUState Key Laboratory of Multi-phase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
Received:2018-06-28Revised:2018-09-04Online:2018-12-22Published:2018-12-19摘要/Abstract
摘要： 蛋白质是生命的物质基础，是生命活动的主要承担者，对蛋白质时空多尺度结构及其控制机制的深入理解是探索生命起源、病理认知及新药开发的基础. 受实验表征手段及时空分辨率的限制，计算机模拟已成为研究蛋白质体系结构及功能的重要手段之一. 由于蛋白质体系模拟所涉及的时间和空间跨度均相当大，因此，准确且快速地描述其时空多尺度结构，从而分析体系的控制机制及相关生理过程，成为分子动力学模拟面临的巨大挑战. 本工作对近半个世纪以来的分子模拟方法，特别是分子动力学方法和相关的增强采样技术在蛋白质体系研究中的应用进行了总结，综述了近年来分子动力学的理论模型和算法的发展，并介绍了这些方法在结构化蛋白质的天然结构与构象变化、固有无序蛋白质的动态结构及其结合底物的动力学过程及分子机理、分子伴侣及病毒等蛋白质复合物体系中的研究成果；汇总了高性能计算的飞速发展所带动的分子动力学模拟软件的变革，拓展了蛋白质模拟的时空尺度，重点阐述了大规模高性能分子动力学模拟在蛋白质研究中的应用；最后，基于介科学理论的飞速发展及其在多种复杂体系的成功运用，对未来蛋白质体系的模拟方法和理论研究的趋势进行了思考和展望.
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任瑛 徐骥. 蛋白质体系分子动力学模拟的前沿进展-从介科学角度重新审视[J]. 过程工程学报, 2018, 18(6): 1126-1137.
Ying REN Ji XU. Frontiers of molecular dynamics simulations of protein systems-reexamine from the mesoscience perspective[J]. Chin. J. Process Eng., 2018, 18(6): 1126-1137.
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