ArticleBMC bioinformatics2010
Detecting internally symmetric protein structures.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- GLMYsymm: inferring symmetry categories of protein complexes from single sequences using persistent GLMY homology.Briefings in bioinformatics · 2026Article
- pLM-Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection.Protein science : a publication of the Protein Society · 2026Article
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- On the emergence of metabolism: the evolution of proteins that powered life.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins.Bioinformatics (Oxford, England) · 2025Article
- Ig or Not Ig? That Is the Question: The Nucleating Supersecondary Structure of the Ig-Fold and the Extended Ig Universe.Methods in molecular biology (Clifton, N.J.) · 2025Article
- EncoMPASS: An encyclopedia of membrane proteins analyzed by structure and symmetry.Structure (London, England : 1993) · 2024Article
- Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins.Journal of molecular evolution · 2020Article
- MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudosymmetries.Journal of molecular biology · 2020Article
- Article
- Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis.Journal of cheminformatics · 2019Article
- Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.PLoS computational biology · 2019Article
- EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins.Nucleic acids research · 2019Article
- Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Identification and Analysis of Long Repeats of Proteins at the Domain Level.Frontiers in bioengineering and biotechnology · 2019Article
- Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains.BioMed research international · 2016Article
- A model for genesis of transcription systems.Transcription · 2016Article
- Article
- Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy.Proteins · 2015Article
- A Suite of Engineered GFP Molecules for Oligomeric Scaffolding.Structure (London, England : 1993) · 2015Article
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3 authors.
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Abstract
backgroundMany functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state. These internally symmetric proteins are interesting objects from the point of view of their folding, function, and evolution. Most algorithms that detect the internally symmetric proteins depend on finding repeating units of similar structure and do not use the symmetry information.
resultsWe describe a new method, called SymD, for detecting symmetric protein structures. The SymD procedure works by comparing the structure to its own copy after the copy is circularly permuted by all possible number of residues. The procedure is relatively insensitive to symmetry-breaking insertions and deletions and amplifies positive signals from symmetry. It finds 70% to 80% of the TIM barrel fold domains in the ASTRAL 40 domain database and 100% of the beta-propellers as symmetric. More globally, 10% to 15% of the proteins in the ASTRAL 40 domain database may be considered symmetric according to this procedure depending on the precise cutoff value used to measure the degree of perfection of the symmetry. Symmetrical proteins occur in all structural classes and can have a closed, circular structure, a cylindrical barrel-like structure, or an open, helical structure.
conclusionsSymD is a sensitive procedure for detecting internally symmetric protein structures. Using this procedure, we estimate that 10% to 15% of the known protein domains may be considered symmetric. We also report an initial, overall view of the types of symmetries and symmetric folds that occur in the protein domain structure universe.
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