Vorolign--fast structural alignment using Voronoi contacts

Vorolign, a fast and flexible structural alignment method for two or more protein structures is introduced. The method aligns protein structures using double dynamic programming and measures the similarity of two residues based on the evolutionary conservation of their corresponding Voronoi-contacts in the protein structure. This similarity function allows aligning protein structures even in cases where structural flexibilities exist. Multiple structural alignments are generated from a set of pairwise alignments using a consistency-based, progressive multiple alignment strategy. RESULTS: The performance of Vorolign is evaluated for different applications of protein structure comparison, including automatic family detection as well as pairwise and multiple structure alignment. Vorolign accurately detects the correct family, superfamily or fold of a protein with respect to the SCOP classification on a set of difficult target structures. A scan against a database of >4000 proteins takes on average 1 min per target. The performance of Vorolign in calculating pairwise and multiple alignments is found to be comparable with other pairwise and multiple protein structure alignment methods. AVAILABILITY: Vorolign is freely available for academic users as a web server at http://www.bio.ifi.lmu.de/Vorolign