Conference proceeding
Protein Structure Comparison and Alignment Using Residue Contexts
2008 22ND INTERNATIONAL WORKSHOPS ON ADVANCED INFORMATION NETWORKING AND APPLICATIONS, VOLS 1-3, pp.796-801
01/01/2008
DOI: 10.1109/WAINA.2008.22
Abstract
We introduce a method for comparing protein structures using the notion of residue contexts based on protein C-alpha-atom backbones. The residue context is derived from the set of vectors from a given C-alpha-atom to each other C-alpha-atom in the molecule. A three-dimensional histogram is generated from these vectors, containing a relative distribution of the other C-alpha-atoms for each C-alpha-atom on the back-bone for a protein. Histograms are compared using the chi(2) test, resulting in the cost for matching any two given C-alpha-atoms in a pair of protein molecules. An optimal alignment is made using the Smith-Waterman algorithm, and a score is calculated based on the length of the alignment and the RMSD, yielding a best alignment that can be displayed in an interactive user interface. Resulting alignments are compared with alignments generated by CTSS, DALI, and CE, yielding different aligned protein regions.
Details
- Title: Subtitle
- Protein Structure Comparison and Alignment Using Residue Contexts
- Creators
- Tobias Sayre - San Francisco State UniversityRahul Singh - San Francisco State University
- Resource Type
- Conference proceeding
- Publication Details
- 2008 22ND INTERNATIONAL WORKSHOPS ON ADVANCED INFORMATION NETWORKING AND APPLICATIONS, VOLS 1-3, pp.796-801
- Publisher
- IEEE
- DOI
- 10.1109/WAINA.2008.22
- ISSN
- 1550-445X
- eISSN
- 2332-5658
- Number of pages
- 2
- Language
- English
- Date published
- 01/01/2008
- Academic Unit
- Computer Science
- Record Identifier
- 9984446278402771
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