Protein structure alignment beyond spatial proximity

Sheng Wang, Jianzhu Ma, Jian Peng, Jinbo Xu

Code and Data Abstract

Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures.


Sheng Wang, Jianzhu Ma, Jian Peng, Jinbo Xu, et al. 2013. "Protein structure alignment beyond spatial proximity." Scientific Reports. 3 1448.    doi:10.1038/srep01448. Retrieved 06/24/2019 from

Compendium Type: Published Papers
Primary Research Field: Computer and Information Sciences
Secondary Research Field: Mathematics
Content License: Public Domain Mark
Code License: MIT License

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created 02/18/2014

modified 02/18/2014

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