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

TitleFr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
Publication TypeJournal Article
Year of Publication2008
AuthorsPandit SB, Skolnick J
JournalBMC Bioinformatics
Volume9
Pagination531
Date Published2008
ISSN1471-2105
KeywordsAlgorithms, Animals, Computational Biology, Computers, Databases, Protein, Humans, Models, Statistical, Molecular Sequence Data, Protein Conformation, Protein Structure, Tertiary, Proteins, Sequence Alignment, Sequence Analysis, Protein, Software
Abstract

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.

Alternate JournalBMC Bioinformatics

© Michal Brylinski
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