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

Jieping Ye, Ravi Janardan, Songtao Liu

Research output: Contribution to journalConference articlepeer-review

2 Scopus citations

Abstract

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 [12] and LOCK [19].

Original languageEnglish (US)
Pages (from-to)2-9
Number of pages8
JournalProceedings of the International Conference on Tools with Artificial Intelligence
StatePublished - Dec 16 2003
EventProceedings: 15th IEEE International Conference on Tools with artificial Intelligence - Sacramento, CA, United States
Duration: Nov 3 2003Nov 5 2003

Keywords

  • Dynamic programming
  • Frobenius norm
  • Rigid motion
  • Root-mean squared deviation
  • Singular value decomposition
  • Structure alignment

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