Pairwise protein structure alignment based on an orientation-independent backbone representation

Jieping Ye, Ravi Janardan, Songtao Liu

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this representation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI and LOCK.

Original languageEnglish (US)
Pages (from-to)699-717
Number of pages19
JournalJournal of Bioinformatics and Computational Biology
Issue number4
StatePublished - Dec 2004


  • Backbone representation
  • Dynamic programming
  • Optimization
  • Protein structure alignment


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