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Multiple structure alignment with msTALI.

Shealy P, Valafar H - BMC Bioinformatics (2012)

Bottom Line: Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification.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.In addition to its performance on standard comparison databases, it utilizes clear, informative features, allowing further customization for domain-specific applications.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA.

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 at http://ifestos.cse.sc.edu/mstali.

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A flowchart of the msTALI algorithm.
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Figure 11: A flowchart of the msTALI algorithm.

Mentions: The core identification wrapper is designed to extract a structural core from a set of homologous proteins. The criterion it optimizes is maximizing the number of residues included in the core with the constraint that the residues (potentially disjoint in sequence) fall under an RMSD cutoff. It is important to observe both of these criteria simultaneously since they are competing objectives. The complete algorithm is shown in Figure11. This algorithm uses several parameters; the automated method for determining these parameters from a set of training examples.


Multiple structure alignment with msTALI.

Shealy P, Valafar H - BMC Bioinformatics (2012)

A flowchart of the msTALI algorithm.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473313&req=5

Figure 11: A flowchart of the msTALI algorithm.
Mentions: The core identification wrapper is designed to extract a structural core from a set of homologous proteins. The criterion it optimizes is maximizing the number of residues included in the core with the constraint that the residues (potentially disjoint in sequence) fall under an RMSD cutoff. It is important to observe both of these criteria simultaneously since they are competing objectives. The complete algorithm is shown in Figure11. This algorithm uses several parameters; the automated method for determining these parameters from a set of training examples.

Bottom Line: Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification.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.In addition to its performance on standard comparison databases, it utilizes clear, informative features, allowing further customization for domain-specific applications.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA.

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 at http://ifestos.cse.sc.edu/mstali.

Show MeSH
Related in: MedlinePlus