摘要
蛋白质结构与功能之间的关系非常密切,蛋白质分子体系中的各种相互作用力在空间叠加形成一个综合性作用(分子场),对揭示蛋白质结构与功能之间的内在关系具有重要意义.提出了基于线性标度量子化学理论的蛋白质分子场快速计算方法,利用分而治之的思想,根据氨基酸残基把一个蛋白质大分子分解成若干片段,然后对每个片段单独计算,最后对各片段的重要区域在空间网格点上进行拼接,获得完整的三维分子场数据;为了提高计算速度,还提出了基于MPICH模型的并行计算方法.实验结果证明,文中方法能实现复杂蛋白质分子的分子场的高效、高精度计算.
It is widely recognized that the function of a protein is dependent on its spatial structure. All kinds of interactions taken place inside the protein are superposed in the space to form a molecular field, which affects the protein function greatly. An algorithm based on linear calibration quantum chemistry theory for fast calculating the molecular field of a protein is presented in this paper. Since the protein molecule is too complex to be computed with the classic quantum chemistry algorithm, we employ the divide-and-conquer strategy to divide the protein into several fragments according to amino acid residue. The computation results on all the fragments are finally integrated by performing interpolation at the overlapped boundary. The whole process is further accelerated by parallel computing based on MPICH. Experimental results demonstrate the effectiveness and efficiency of our approach.
出处
《计算机辅助设计与图形学学报》
EI
CSCD
北大核心
2008年第9期1238-1245,共8页
Journal of Computer-Aided Design & Computer Graphics
基金
国家自然科学基金重点项目(60533050)
国家自然科学基金(60673063)
关键词
氨基酸残基
分而治之
并行计算
分子场
amino acid residue
divide and conquer
parallel computation
molecular field
