ArticleBioinformatics (Oxford, England)2016
Revealing aperiodic aspects of solenoid proteins from sequence information.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- PRIGSA2: Improved version of protein repeat identification by graph spectral analysis.Journal of biosciences · 2020Article
- Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments.Pharmaceuticals (Basel, Switzerland) · 2017Article
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Authors and funding
3 authors.
Funding
Abstract
motivationRepeat proteins, which contain multiple repeats of short sequence motifs, form a large but seldom-studied group of proteins. Methods focusing on the analysis of 3D structures of such proteins identified many subtle effects in length distribution of individual motifs that are important for their functions. However, similar analysis was yet not applied to the vast majority of repeat proteins with unknown 3D structures, mostly because of the extreme diversity of the underlying motifs and the resulting difficulty to detect those.
resultsWe developed FAIT, a sequence-based algorithm for the precise assignment of individual repeats in repeat proteins and introduced a framework to classify and compare aperiodicity patterns for large protein families. FAIT extracts repeat positions by post-processing FFAS alignment matrices with image processing methods. On examples of proteins with Leucine Rich Repeat (LRR) domains and other solenoids like proteins, we show that the automated analysis with FAIT correctly identifies exact lengths of individual repeats based entirely on sequence information. AVAILABILITY AND IMPLEMENTATION: https://github.com/GodzikLab/FAIT CONTACT: adam@godziklab.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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