ArticleBMC bioinformatics2014
ConSole: using modularity of contact maps to locate solenoid domains in protein structures.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Unusual structural and functional features of TpLRR/BspA-like LRR proteins.Journal of structural biology · 2023Review
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- RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures.Nucleic acids research · 2021Article
- MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudosymmetries.Journal of molecular biology · 2020Article
- PRIGSA2: Improved version of protein repeat identification by graph spectral analysis.Journal of biosciences · 2020Article
- Novel Descriptors and Digital Signal Processing- Based Method for Protein Sequence Activity Relationship Study.International journal of molecular sciences · 2019Article
- Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.PLoS computational biology · 2019Article
- A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes.Scientific reports · 2018Article
- RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.Nucleic acids research · 2018Article
- Article
- VLR Recognition of TLR5 Expands the Molecular Characterization of Protein Antigen Binding by Non-Ig-based Antibodies.Journal of molecular biology · 2018Article
- RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.Nucleic acids research · 2017Article
- Revealing aperiodic aspects of solenoid proteins from sequence information.Bioinformatics (Oxford, England) · 2016Article
- NAPS: Network Analysis of Protein Structures.Nucleic acids research · 2016Article
- Structural and Energetic Characterization of the Ankyrin Repeat Protein Family.PLoS computational biology · 2015Article
- Tandem Repeats in Proteins: Prediction Algorithms and Biological Role.Frontiers in bioengineering and biotechnology · 2015Review
- Identifying tandem Ankyrin repeats in protein structures.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundPeriodic 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.
resultsConSole 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.
conclusionsThe 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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