ArticleProtein science : a publication of the Protein Society2019
The Urfold: Structural similarity just above the superfold level?
Article in Protein science : a publication of the Protein Society, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Deep generative models of protein structure uncover distant relationships across a continuous fold space.Nature communications · 2024Article
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- The curse of the protein ribbon diagram.PLoS biology · 2022Article
- BioS2Net: Holistic Structural and Sequential Analysis of Biomolecules Using a Deep Neural Network.International journal of molecular sciences · 2022Article
- The Urfold: Structural similarity just above the superfold level?Protein science : a publication of the Protein Society · 2019Article
- Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways.PLoS computational biology · 2019Article
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3 authors.
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Abstract
We suspect that there is a level of granularity of protein structure intermediate between the classical levels of "architecture" and "topology," as reflected in such phenomena as extensive three-dimensional structural similarity above the level of (super)folds. Here, we examine this notion of architectural identity despite topological variability, starting with a concept that we call the "Urfold." We believe that this model could offer a new conceptual approach for protein structural analysis and classification: indeed, the Urfold concept may help reconcile various phenomena that have been frequently recognized or debated for years, such as the precise meaning of "significant" structural overlap and the degree of continuity of fold space. More broadly, the role of structural similarity in sequence↔structure↔function evolution has been studied via many models over the years; by addressing a conceptual gap that we believe exists between the architecture and topology levels of structural classification schemes, the Urfold eventually may help synthesize these models into a generalized, consistent framework. Here, we begin by qualitatively introducing the concept.
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