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Protein structure alignment using geometrical features

Published: 13 November 2004 Publication History

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.

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Cited By

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  • (2011)Sequence Order Independent Comparison of Protein Global Backbone Structures and Local Binding Surfaces for Evolutionary and Functional InferenceProtein Function Prediction for Omics Era10.1007/978-94-007-0881-5_7(125-143)Online publication date: 29-Mar-2011
  • (2007)Common Substructure Extraction of Proteins by Geometric Invariants2007 10th IEEE International Conference on Computer-Aided Design and Computer Graphics10.1109/CADCG.2007.4407861(86-91)Online publication date: Oct-2007
  • (2006)Construction of Protein Structure Spectrum Under United Coordinates2006 International Conference on Mechatronics and Automation10.1109/ICMA.2006.257582(2013-2017)Online publication date: Dec-2006
  • Show More Cited By

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cover image ACM Conferences
CIKM '04: Proceedings of the thirteenth ACM international conference on Information and knowledge management
November 2004
678 pages
ISBN:1581138741
DOI:10.1145/1031171
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 13 November 2004

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Author Tags

  1. biological data mining
  2. biological databases
  3. protein structure alignment
  4. shape similarity

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CIKM04
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CIKM04: Conference on Information and Knowledge Management
November 8 - 13, 2004
D.C., Washington, USA

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Overall Acceptance Rate 1,861 of 8,427 submissions, 22%

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Cited By

View all
  • (2011)Sequence Order Independent Comparison of Protein Global Backbone Structures and Local Binding Surfaces for Evolutionary and Functional InferenceProtein Function Prediction for Omics Era10.1007/978-94-007-0881-5_7(125-143)Online publication date: 29-Mar-2011
  • (2007)Common Substructure Extraction of Proteins by Geometric Invariants2007 10th IEEE International Conference on Computer-Aided Design and Computer Graphics10.1109/CADCG.2007.4407861(86-91)Online publication date: Oct-2007
  • (2006)Construction of Protein Structure Spectrum Under United Coordinates2006 International Conference on Mechatronics and Automation10.1109/ICMA.2006.257582(2013-2017)Online publication date: Dec-2006
  • (2005)PADSProceedings of the 10th international conference on Database Systems for Advanced Applications10.1007/11408079_5(17-29)Online publication date: 17-Apr-2005

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