Protein structure alignment using geometrical features

S. Alireza Aghili, Divyakant Agrawal, Amr El Abbadi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

A novel approach for similarity search on protein structure databases is proposed which incorporates the three dimensional coordinates of the main atoms of each amino acid and extracts a geometrical signature along with the direction of the given amino acid. As a result, each protein is presented by a series of feature vectors representing local geometry, shape, direction, and secondary structure assignment of its amino acid constituents. Furthermore, a residue-to-residue distance matrix is calculated and is incorporated into a local alignment dynamic programming algorithm to find the similar portions of two given proteins and finally a sequence alignment step is used as the last filtration step. The optimal superimposition of the detected similar regions is used to assess the quality of the results. The proposed algorithm is fast and accurate and hence could be used for the analysis of large protein structure similarity.

Original languageEnglish
Title of host publicationInternational Conference on Information and Knowledge Management, Proceedings
EditorsD.A. Evans, L. Gravano, O. Herzog, C. Zhai, M. Ronthaler
Pages148-149
Number of pages2
Publication statusPublished - 1 Dec 2004
Externally publishedYes
EventCIKM 2004: Proceedings of the Thirteenth ACM Conference on Information and Knowledge Management - Washington, DC, United States
Duration: 8 Nov 200413 Nov 2004

Other

OtherCIKM 2004: Proceedings of the Thirteenth ACM Conference on Information and Knowledge Management
CountryUnited States
CityWashington, DC
Period8/11/0413/11/04

Fingerprint

Protein
Alignment
Data base
Geometry
Similarity search
Dynamic programming
Assignment

Keywords

  • Biological Data Mining
  • Biological Databases
  • Protein Structure Alignment
  • Shape Similarity

ASJC Scopus subject areas

  • Business, Management and Accounting(all)

Cite this

Aghili, S. A., Agrawal, D., & Abbadi, A. E. (2004). Protein structure alignment using geometrical features. In D. A. Evans, L. Gravano, O. Herzog, C. Zhai, & M. Ronthaler (Eds.), International Conference on Information and Knowledge Management, Proceedings (pp. 148-149)

Protein structure alignment using geometrical features. / Aghili, S. Alireza; Agrawal, Divyakant; Abbadi, Amr El.

International Conference on Information and Knowledge Management, Proceedings. ed. / D.A. Evans; L. Gravano; O. Herzog; C. Zhai; M. Ronthaler. 2004. p. 148-149.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Aghili, SA, Agrawal, D & Abbadi, AE 2004, Protein structure alignment using geometrical features. in DA Evans, L Gravano, O Herzog, C Zhai & M Ronthaler (eds), International Conference on Information and Knowledge Management, Proceedings. pp. 148-149, CIKM 2004: Proceedings of the Thirteenth ACM Conference on Information and Knowledge Management, Washington, DC, United States, 8/11/04.
Aghili SA, Agrawal D, Abbadi AE. Protein structure alignment using geometrical features. In Evans DA, Gravano L, Herzog O, Zhai C, Ronthaler M, editors, International Conference on Information and Knowledge Management, Proceedings. 2004. p. 148-149
Aghili, S. Alireza ; Agrawal, Divyakant ; Abbadi, Amr El. / Protein structure alignment using geometrical features. International Conference on Information and Knowledge Management, Proceedings. editor / D.A. Evans ; L. Gravano ; O. Herzog ; C. Zhai ; M. Ronthaler. 2004. pp. 148-149
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