Integrated search and alignment of protein structures

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2008-12-15

Author

Sacan, Ahmet
Toroslu, İsmail Hakkı
Ferhatosmanoglu, Hakan

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Motivation: 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.

Subject Keywords

Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications

URI

https://hdl.handle.net/11511/37309

Journal

BIOINFORMATICS

DOI

https://doi.org/10.1093/bioinformatics/btn545

Collections

Department of Computer Engineering, Article

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Citation Formats

A. Sacan, İ. H. Toroslu, and H. Ferhatosmanoglu, “Integrated search and alignment of protein structures,” BIOINFORMATICS, pp. 2872–2879, 2008, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/37309.