ReviewCurrent opinion in structural biology2009
Discrete-continuous duality of protein structure space.
Review in Current opinion in structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
38 citing papers in PubMed.
- Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins.Protein science : a publication of the Protein Society · 2025Article
- Refinement and curation of homologous groups facilitated by structure prediction.Protein science : a publication of the Protein Society · 2025Article
- Deep generative models of protein structure uncover distant relationships across a continuous fold space.Nature communications · 2024Article
- GTalign: spatial index-driven protein structure alignment, superposition, and search.Nature communications · 2024Article
- Fluid protein fold space and its implications.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Classification of domains in predicted structures of the human proteome.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A review of visualisations of protein fold networks and their relationship with sequence and function.Biological reviews of the Cambridge Philosophical Society · 2023Review
- The curse of the protein ribbon diagram.PLoS biology · 2022Article
- The Urfold: Structural similarity just above the superfold level?Protein science : a publication of the Protein Society · 2019Article
- Unraveling the structural landscape of intra-chain domain interfaces: Implication in the evolution of domain-domain interactions.PloS one · 2019Article
- Multistep mutational transformation of a protein fold through structural intermediates.Protein science : a publication of the Protein Society · 2018Article
- Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds.Proteins · 2016Article
- Diversity in protein domain superfamilies.Current opinion in genetics & development · 2015Review
- Nonlinearities in protein space limit the utility of informatics in protein biophysics.Proteins · 2015Article
- Structural Bridges through Fold Space.PLoS computational biology · 2015Article
- A new method to improve network topological similarity search: applied to fold recognition.Bioinformatics (Oxford, England) · 2015Article
- Smooth functional transition along a mutational pathway with an abrupt protein fold switch.Biophysical journal · 2014Article
- Global view of the protein universe.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Systematic detection of internal symmetry in proteins using CE-Symm.Journal of molecular biology · 2014Article
- How a spatial arrangement of secondary structure elements is dispersed in the universe of protein folds.PloS one · 2014Article
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3 authors.
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Abstract
Recently, the nature of protein structure space has been widely discussed in the literature. The traditional discrete view of protein universe as a set of separate folds has been criticized in the light of growing evidence that almost any arrangement of secondary structures is possible and the whole protein space can be traversed through a path of similar structures. Here we argue that the discrete and continuous descriptions are not mutually exclusive, but complementary: the space is largely discrete in evolutionary sense, but continuous geometrically when purely structural similarities are quantified. Evolutionary connections are mainly confined to separate structural prototypes corresponding to folds as islands of structural stability, with few remaining traceable links between the islands. However, for a geometric similarity measure, it is usually possible to find a reasonable cutoff that yields paths connecting any two structures through intermediates.
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