@article {bioinflmu-613,
	title = {{Vorolign - Fast Structural Alignment using Voronoi Contacts}},
	journal = {Bioinformatics},
	volume = {23},
	number = {2},
	year = {2007},
	pages = {e205-e211},
	abstract = {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},
	keywords = {vorolign-07, vorolignServer},
	doi = {10.1093/bioinformatics/btl294},
	url1 = {<a href="http://www2.bio.ifi.lmu.de/Vorolign/">Vorolign Homepage</a>},
	author = {Fabian Birzele and Jan Erik Gewehr and Gergely Csaba and Ralf Zimmer}
}