Integrated search and alignment of protein structures

Sacan, Ahmet
Toroslu, İsmail Hakkı
Ferhatosmanoglu, Hakan
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.
Citation Formats
A. Sacan, İ. H. Toroslu, and H. Ferhatosmanoglu, “Integrated search and alignment of protein structures,” BIOINFORMATICS, vol. 24, no. 24, pp. 2872–2879, 2008, Accessed: 00, 2020. [Online]. Available: