Multiple structure alignment with msTALI

Abstract

BackgroundMultiple 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.ResultsmsTALI 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.ConclusionsmsTALI 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 at http://ifestos.cse.sc.edu/mstali.

PDBMine: A Reformulation of the Protein Data Bank to Facilitate Structural Data Mining

“…This bb-RMSD indicates a reasonably high level of similarity between the two structures. Further analysis using multiple structure alignment software msTALI [7,8] showed that the conserved core between these three structures (k=6,7 and the x-ray) contained 57 residues. The remaining 19 residues contributed to the divergence in structure (bb-RMSD).…”

Evaluating Precisicon and Recall through the Utility of msTALI via an Active Site Study on Fold Families

“…The phylogenetic analysis feature of msTALI and its significance has been previously reported [17]. It is important to note that the phylogenetic analysis of msTALI is based on all encompassing features of the proteins including sequence, structure, and other biochemical properties [17]. To clarify further, by excluding all the information except the protein sequences, the results of msTALI will converge to that of ClustalW [25].…”

“…Prior to investigating the output generated by our multiple structure alignment with msTALI it is important to establish the legitimacy of its alignment [1]. The phylogenetic analysis feature of msTALI and its significance has been previously reported [17]. It is important to note that the phylogenetic analysis of msTALI is based on all encompassing features of the proteins including sequence, structure, and other biochemical properties [17].…”

Multiple Alignment of Structures Using Center Of ProTeins

“…Multiple Structure Alignment (MStA) of protein structures can be categorized into four widely different approaches -progressive alignment, core optimization, graph based, and pivot based. Mustang [13], msTali [23] , mulPBA [14], and CE-MC [7] use the progressive alignment approach that creates an alignment of alignments following a guide tree. While this approach does make sense, it suffers from the natural disadvantages of all progressive techniques.…”