文献类型：期刊文献

英文题名：Molecular docking simulation based on CPU-GPU heterogeneous computing

作者：Xu, Jinyan[1]; Li, Jianhua[1]; Cai, Yining[1]

机构：[1] Department of Computer Science and Engineering, East China University of Science and Technology, Shanghai, China

年份：2017

卷号：10561 LNCS

起止页码：27

外文期刊名：Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

收录：EI(收录号：20174004226356)

语种：英文

外文关键词：Electronic data interchange - Free energy - Genetic algorithms - Binding energy - Molecular modeling

摘要：Receptor-ligand molecular docking aims to predict possible drug candidates for many diseases, and it requires a lot of computing cost. Shortening this time- consumption process will help pharmaceutical scientist to speed up drug development. In this paper, a parallel molecular docking simulation based on CPU-GPU heterogeneous computing is proposed. This simulation is developed from our previous developed molecular docking code iFitDock (Induced fit docking program) which introduced Non-dominated Sorting Genetic Algorithm II (NSGA II) and Molecular Mechanical-Generalized Born Surface Area (MM-GBSA) binding free energy. In this program, the most computationally intensive part is the computing of scoring functions due to complex computing process of free binding free energy. Thus, this paper focuses on offloading the computing of scoring functions as well as related conformation spatial transformation to GPU, and keeping the rest of the simulation on CPU. A detailed CPU-GPU heterogeneous computing model is constructed to parallelize the computing of scoring functions and related workload on the GPU and to define the data exchange between GPU and CPU. The primary parallel iFitDock system with only parallel semi-flexible docking implemented achieves a speedup of around ~20× with respect to a single CPU core. The result shows that it is very productive to use CPU-GPU heterogeneous computing for semi-flexible molecule docking cases in iFitDock. ? 2017, Springer International Publishing AG.