A new algorithm for sequential and non-sequential protein multiple structure alignment
A fundamental issue in studies of protein structure and function is how to identify the conserved common core in multiple protein structures. The existing algorithms work well for proteins family such as those in HOMSTRAD but are not satisfactory for general multiple structure alignment problems, especially in some challenging cases, such as the occurrence of circular permutations. In this paper, an efficient approach called SANA-mult for multiple structure alignment is presented. Specifically, the alignment problem is first mapped on to a mixed integer programming problem via introducing a structural template, and then the algorithm decomposes the problem into two subproblems, i.e. solving the pairwise alignment and updating the template chain. We show that the proposed method can obtain sequential and non-sequential solutions for multiple structure alignment in an accurate manner, which is competitive or superior to the existing methods. The effectiveness of the new algorithm SANA-mult is tested using various protein structure sets and benchmark examples.
Protein structure multiple structure alignment circular permutation sequential alignment non-sequential alignment.
Lin Wang Wen-Juan Zhang
institute of Applied Mathematics, Academy of Mathematics and Systems Science Chinese Academy of Scie Department of Basic Courses, Tianjin Foreign Studies University, Tianjin 300204, China
国际会议
The Second International Symposium(OSB08)(第二届国际优化及系统生物学学术会议)
云南丽江
英文
83-90
2008-10-31（万方平台首次上网日期，不代表论文的发表时间）