A Database of Pairwise Aligned 3-D Structures for the Acetylcholinesterases, Lipases and Other Homologous Proteins

The comparison of results from 3-D structure alignments obtained by a variety of different algorithms and those determined by domain experts reveals significant differences. Simply finding the best RMSD between the corresponding C α positions in two structures is not enough to match biologically meaningful features, and hence provide the most meaningful structure alignment. Yet an accurate comparative analysis of structure reveals a great deal about the biological function of related proteins. A recently described combinatorial extension algorithm has been further refined by the use of protein properties relevant to structural and functional features to provide good structure alignments. The resulting database of automated pairwise alignments is reported and contains acetylcholinesterases (9), lipases (15), haloalkane dehalogenases (11), and cholesterol esterases (2) structures for which more than 200 residues could be aligned with an RMSD of less than 4.0A. Results for the alignment of a specific acetylcholinesterase to a lipase is compared to the previously performed manual alignment. The database and associated tools for visualizing the structure alignments are available via the Web at the URL http://cl.sdsc.edu/align_db.html.