Journal article
Integrated search and alignment of protein structures
Bioinformatics (Oxford, England), v 24(24), pp 2872-2879
15 Dec 2008
PMID: 18945684
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The contact hits obtained from a distance-based indexing method are extended to obtain high-scoring segment pairs, which are then used to generate structural alignments.
Vorometric is the first to address both search and alignment problems in the protein structure databases. The experimental results show that Vorometric is simultaneously effective in retrieving similar protein structures, producing high-quality structure alignments, and identifying cross-fold similarities. Vorometric outperforms current structure retrieval methods in search accuracy, while requiring com-parable running times. Furthermore, the structural superpositions produced are shown to have better quality and coverage, when compared with those of the popular structure alignment tools.
Vorometric is available as a web service at http://bio.cse.ohio-state.edu/Vorometric
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Details
- Title
- Integrated search and alignment of protein structures
- Creators
- Ahmet Sacan - Department of Computer Engineering, Middle East Technical University, Ankara, Turkey. sacan@cse.ohio-state.eduI Hakki TorosluHakan Ferhatosmanoglu
- Publication Details
- Bioinformatics (Oxford, England), v 24(24), pp 2872-2879
- Publisher
- Oxford University Press; England
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000261456700010
- Scopus ID
- 2-s2.0-57249083981
- Other Identifier
- 991014878392904721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemical Research Methods
- Biotechnology & Applied Microbiology
- Computer Science, Interdisciplinary Applications
- Mathematical & Computational Biology
- Statistics & Probability