关键词: 生物计算, 第一性原理, 并行计算, 分子对接, 蛋白质识别

Abstract: It has been found that key area research during protein recognition process is typically important for proclaiming biological phenomena essence, improving drug design efficiency and decreasing cost and shortening industrial cycle of new drug design. For high complexity of protein macromolecule structure, common computer systems are not capable for continuously tracking coherence change of structure and function during protein recognition. This paper sets up a heterogeneous cluster based on GPU/CPU as a uniform biological computing environment, proposes particular data structures and algorithms to deal with large biological data, and reconfigures Kd-tree based on GPU and data access modes to improve parallel calculation performance. Thus it becomes feasible to calculate time-varying protein molecular filed fast enough to do further analysis on key area for protein recognition. The corresponding biochemistry experiment results show that the method can be used as a new effective and intuitive tool for protein interaction research.

Key words: biological computation, first principle, parallel calculation, molecular docking, protein recognition