Runze Dong1, Zhenling Peng2, Yang Zhang3, Jianyi Yang1. 1. School of Mathematical Sciences, Nankai University, Tianjin 300071, China. 2. Center for Applied Mathematics, Tianjin University, Tianjin 300072, China. 3. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.
Abstract
Motivation: As protein structure is more conserved than sequence during evolution, multiple structure alignment can be more informative than multiple sequence alignment, especially for distantly related proteins. With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop efficient algorithms for multiple structure alignment. Results: A new multiple structure alignment algorithm (mTM-align) was proposed, which is an extension of the highly efficient pairwise structure alignment program TM-align. The algorithm was benchmarked on four widely used datasets, HOMSTRAD, SABmark_sup, SABmark_twi and SISY-multiple, showing that mTM-align consistently outperforms other algorithms. In addition, the comparison with the manually curated alignments in the HOMSTRAD database shows that the automated alignments built by mTM-align are in general more accurate. Therefore, mTM-align may be used as a reliable complement to construct multiple structure alignments for real-world applications. Availability and implementation: http://yanglab.nankai.edu.cn/mTM-align. Contact: zhng@umich.edu or yangjy@nankai.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: As protein structure is more conserved than sequence during evolution, multiple structure alignment can be more informative than multiple sequence alignment, especially for distantly related proteins. With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop efficient algorithms for multiple structure alignment. Results: A new multiple structure alignment algorithm (mTM-align) was proposed, which is an extension of the highly efficient pairwise structure alignment program TM-align. The algorithm was benchmarked on four widely used datasets, HOMSTRAD, SABmark_sup, SABmark_twi and SISY-multiple, showing that mTM-align consistently outperforms other algorithms. In addition, the comparison with the manually curated alignments in the HOMSTRAD database shows that the automated alignments built by mTM-align are in general more accurate. Therefore, mTM-align may be used as a reliable complement to construct multiple structure alignments for real-world applications. Availability and implementation: http://yanglab.nankai.edu.cn/mTM-align. Contact: zhng@umich.edu or yangjy@nankai.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.
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