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We are analyzing https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-119.

Title:
ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures | BMC Bioinformatics | Full Text
Description:
Background Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins. Results ConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families. Conclusions The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org .
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25 years and 10 months (reg. 1999-08-06).

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Keywords {🔍}

solenoid, protein, structures, structure, repeats, article, residues, proteins, units, contact, google, scholar, pubmed, classification, repeat, cas, detection, figure, console, unit, correlation, sequence, motif, structural, results, length, determined, analysis, motifs, individual, nonsolenoid, based, residue, lrr, bioinformatics, alignment, authors, maps, recognition, solenoids, benchmark, pattern, main, irregularities, families, ankyrin, size, file, irregularity, bmc,

Topics {✒️}

/academic/subjects/engineering/image-processing machine-vision/correlation-pattern-recognition appended machine-learning classification keywords “jrnl ref popular image-processing procedure simultaneous high-significance matches server page http support vector machine α-helical contact range 𝜎 𝐼 𝑥 large-scale analysis enabled rule-based classifier analyzing privacy choices/manage cookies leucine-rich repeat structure machine-learning algorithms bmc bioinformatics 15 machine-learning method predicting inter-residue contacts article hrabe unit-length irregularity measured bmc bioinforma support vector classification subsequent structural alignment unit-length irregularity distribution fp immunoglobulin a1 proteases armadillo-repeat protein functions authors scientific editing machine learning contact map definition specific solenoid length full size image authors’ original file template-matching algorithm tn leucine rich repeat leucine-rich repeat original annotators postulate find specific patterns frequent contact length discrete fourier transform contact map analysis bmc unusually flat lrr automatically detected λ console-based classification results 𝑗 𝑆 𝑖 cambridge university press methods mol biol unit-length irregularities

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