Document Type
Article
Abstract
Background
Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that is capable of solving a variety of problems using structure comparison is still absent. Here we introduce a program msTALI for aligning multiple protein structures. Our algorithm uses several informative features to guide its alignments: torsion angles, backbone Cα atom positions, secondary structure, residue type, surface accessibility, and properties of nearby atoms. The algorithm allows the user to weight the types of information used to generate the alignment, which expands its utility to a wide variety of problems.
Results
msTALI exhibits competitive results on 824 families from the Homstrad and SABmark databases when compared to Matt and Mustang. We also demonstrate success at building a database of protein cores using 341 randomly selected CATH domains and highlight the contribution of msTALI compared to the CATH classifications. Finally, we present an example applying msTALI to the problem of detecting hinges in a protein undergoing rigid-body motion.
Conclusions
msTALI is an effective algorithm for multiple structure alignment. In addition to its performance on standard comparison databases, it utilizes clear, informative features, allowing further customization for domain-specific applications. The C++ source code for msTALI is available for Linux on the web athttp://ifestos.cse.sc.edu/mstali webcite.
Publication Info
Published in BMC Bioinformatics, Volume 13, Issue May, 2012, pages 105-.
Rights
©BMC Bioinformatics 2012, BioMed Central.
Shealy, P. & Valafar, H. (20 May 2012). Multiple Structure Alignment with msTALI. BMC Bioinformatics 13 (May), 105. http://dx.doi.org/10.1186/1471-2105-13-105