高性能分子动力学模拟在生物大分子结构和功能研究中的应用

Studying Structure and Function Relationship of Biomolecules via High Performance Molecular Dynamics Simulations

基于经典物理学理论的分子动力学模拟是研究生物大分子结构和功能的重要工具。然而,分子动力学模拟对计算资源的巨大需求,限制了其在生物领域的应用。近几年来,随着计算机科学的迅猛发展以及计算化学理论和方法的完善,进行生物大分子在溶液状态下微秒时间尺度的模拟具备了可行性。本篇综述主要介绍近期高性能分子动力学模拟的发展,及在蛋白质三维结构、动态构象变化和生物学功能上的具体应用实例。

State of the art molecular dynamics simulation techniques apply the laws of physics to study structure function relationships of biological macromolecules of interest, which enable us to acquire information not obtainable by experimental techniques and to investigate structural phenomena at the atomic level. Recent advances in computer science and algorithm development make the microsecond timescale simulations on tens of thousands of atoms practical. Here, we highlight the most recent progresses in high performance molecular dynamics simulations and briefly introduce several application projects in studying protein structure, dynamics and biological function.