ArticleThe journal of physical chemistry. B2013
Detecting repetitions and periodicities in proteins by tiling the structural space.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- Frustration in physiology and molecular medicine.Molecular aspects of medicine · 2025Review
- Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer.Science advances · 2022Article
- Resolving the fine structure in the energy landscapes of repeat proteins.QRB discovery · 2022Article
- RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures.Nucleic acids research · 2021Article
- The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins.Frontiers in bioinformatics · 2021Review
- MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudosymmetries.Journal of molecular biology · 2020Article
- Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.PLoS computational biology · 2019Article
- On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences.The journal of physical chemistry. B · 2018Article
- Inferring repeat-protein energetics from evolutionary information.PLoS computational biology · 2017Article
- 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
- Protein Repeats from First Principles.Scientific reports · 2016Article
- Structural and Energetic Characterization of the Ankyrin Repeat Protein Family.PLoS computational biology · 2015Article
- Capturing coevolutionary signals inrepeat proteins.BMC bioinformatics · 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
- Frustration in biomolecules.Quarterly reviews of biophysics · 2014Review
- ConSole: using modularity of contact maps to locate solenoid domains in protein structures.BMC bioinformatics · 2014Article
- NMR contributions to structural dynamics studies of intrinsically disordered proteins.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2014Review
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Authors and funding
5 authors.
Funding
Abstract
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy landscape theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric, we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association toward higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information, we can identify structural units that can be encoded by a variety of distinct amino acid sequences.
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