ArticleProtein science : a publication of the Protein Society2009
Accuracy analysis of multiple structure alignments.
Article in Protein science : a publication of the Protein Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Grafting Methionine on 1F1 Ab Increases the Broad-Activity on HA Structural-Conserved Residues of H1, H2, and H3 Influenza a Viruses.Evolutionary bioinformatics online · 2021Article
- mTM-align: an algorithm for fast and accurate multiple protein structure alignment.Bioinformatics (Oxford, England) · 2018Article
- Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes.PLoS computational biology · 2016Article
- PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.Nucleic acids research · 2016Article
- Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy.Proteins · 2015Article
- WEBnm@ v2.0: Web server and services for comparing protein flexibility.BMC bioinformatics · 2014Article
- A local average distance descriptor for flexible protein structure comparison.BMC bioinformatics · 2014Article
- Vig r 6, the cytokinin-specific binding protein from mung bean (Vigna radiata) sprouts, cross-reacts with Bet v 1-related allergens and binds IgE from birch pollen allergic patients' sera.Molecular nutrition & food research · 2014Article
- MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments.BMC bioinformatics · 2013Article
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- CSA: comprehensive comparison of pairwise protein structure alignments.Nucleic acids research · 2012Article
- A mathematical framework for protein structure comparison.PLoS computational biology · 2011Article
- Touring protein space with Matt.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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3 authors.
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Abstract
Protein structure alignment methods are essential for many different challenges in protein science, such as the determination of relations between proteins in the fold space or the analysis and prediction of their biological function. A number of different pairwise and multiple structure alignment (MStA) programs have been developed and provided to the community. Prior knowledge of the expected alignment accuracy is desirable for the user of such tools. To retrieve an estimate of the performance of current structure alignment methods, we compiled a test suite taken from literature and the SISYPHUS database consisting of proteins that are difficult to align. Subsequently, different MStA programs were evaluated regarding alignment correctness and general limitations. The analysis shows that there are large differences in the success between the methods in terms of applicability and correctness. The latter ranges from 44 to 75% correct core positions. Taking only the best method result per test case this number increases to 84%. We conclude that the methods available are applicable to difficult cases, but also that there is still room for improvements in both, practicability and alignment correctness. An approach that combines the currently available methods supported by a proper score would be useful. Until then, a user should not rely on just a single program.
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