Integrated search and alignment of protein structures

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Abstract

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.

Results

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.

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