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Parallelism of Clonal Selection for PSP on CUDA

Hongbing Zhu, Heng Xiao, JinGuang Gu
Coll. of Comput. Sci. & Technol., Wuhan Univ. of Sci. & Technol., Wuhan, China
3rd International Conference on Intelligent Networks and Intelligent Systems (ICINIS), 2010

@inproceedings{zhu2010parallelism,

   title={Parallelism of Clonal Selection for PSP on CUDA},

   author={Zhu, H. and Xiao, H. and Gu, J.G.},

   booktitle={2010 Third International Conference on Intelligent Networks and Intelligent Systems},

   pages={467–470},

   year={2010},

   organization={IEEE}

}

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Protein structure prediction (PSP) is the process of searching for the min energy of the protein. While many algorithms have being put forward to predict the structure of protein, the complicated computation make the time cost of the algorithms are significantly expensive. CUDA, the newly developing technology, makes us use Graphic Processing Unit (GPU) that is mainly used on Graphic processing at before, much better to develop the general parallel program. So, it gives us a new direction to study the parallelism on PSP. In this paper, we select the clonal selection algorithm for PSP on AB Off-Lattice model and have attempted to fulfill it on the CUDA platform. The results from the experiments showed that it reduced the time cost of the algorithm greatly with a suitable precision. It also provides us a new beginning of the research on PSP.
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