中文摘要：

计算机模拟已发展为根据生物分子结构和动力学阐释生物功能的重要工具.同现有实验比较,计算机模拟不仅能提供结构的时空平均,而且可获得任意微观量的时空分布和演化轨迹.除结构之外,生物功能往往依赖于对动力学的控制.计算机模拟可用于重构构象跃迁路径,发现中间体和过渡态等.本文总结了作者实验室在这一领域的近期工作,特别是关于能量模型、酶催化模拟、构象空间采样等.

英文摘要：

Computer simulation has been developed into an important tool for the elucidation of biological functions from the atomic level structures and dynamics of biomolecules. Compared with current experimental techniques probing atomic level structures, simulations provide not only averages, but also distributions. Besides structures, biological functions often rely on sophisticatedly controlled dynamics of biomolecules, such as the allosteric effects in enzyme catalysis or the effects of ligand-receptor binding in signal transduction. To help understand and eventually control such processes, simulations can be used to reconstruct conformational pathways, identifying intermediates and transition states. This report highlights our recent work in this field. One focus of our research is on developing, testing and refining energy functions for protein simulations, including pure molecular mechanical models for modeling conformational dynamics and hybrid quantum mechanical/molecular mechanical models for modeling enzyme catalysis. Another focus is on developing methods for efficient sampling in the conformational space and for mapping conformational pathways.