Title:
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

dc.contributor.author Pandit, Shashi Bhushan
dc.contributor.author Skolnick, Jeffrey
dc.contributor.corporatename Georgia Institute of Technology. Center for the Study of Systems Biology
dc.date.accessioned 2009-05-14T19:39:04Z
dc.date.available 2009-05-14T19:39:04Z
dc.date.issued 2008-12-12
dc.description ©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531 en
dc.description doi:10.1186/1471-2105-9-531
dc.description.abstract Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/. en
dc.identifier.citation BMC Genomics 2008, 9:531 en
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/1853/27924
dc.language.iso en_US en
dc.publisher Georgia Institute of Technology en
dc.publisher.original BioMed Central
dc.subject Fr-TM-align algorithm
dc.subject Protein tertiary structure comparisons
dc.subject Protein structure comparison metrics
dc.subject TM-score
dc.subject Protein structure comparison
dc.title Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score en
dc.type Text
dc.type.genre Article
dspace.entity.type Publication
local.contributor.author Skolnick, Jeffrey
local.contributor.corporatename College of Sciences
local.contributor.corporatename School of Biological Sciences
local.contributor.corporatename Center for the Study of Systems Biology
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relation.isOrgUnitOfPublication d3d635bd-b38e-4ef6-a2d0-0875b9a83e34
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