ArticleScientific reports2017
Exploring the dark foldable proteome by considering hydrophobic amino acids topology.
Article in Scientific reports, 2017. 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.
- Shining light on the dark proteome with unstructural biology.Current research in structural biology · 2026Article
- Impact of GC content on de novo gene birth.Nature communications · 2026Article
- The Analysis ofCurrent issues in molecular biology · 2025Article
- Learning Universal Representations of Intermolecular Interactions with ATOMICA.bioRxiv : the preprint server for biology · 2025Article
- The evolution of analytical techniques for multiplex analysis of protein biomarkers.Expert review of proteomics · 2025Review
- Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features.Nature communications · 2024Article
- Digging into the 3D Structure Predictions of AlphaFold2 with Low Confidence: Disorder and Beyond.Biomolecules · 2022Article
- Article
- Intrinsically Disordered Proteins: Critical Components of the Wetware.Chemical reviews · 2022Review
- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.Genome research · 2021Article
- Dark Proteome Database: Studies on Dark Proteins.High-throughput · 2019Article
- Discovery and Evolution of New Domains in Yeast Heterochromatin Factor Sir4 and Its Partner Esc1.Genome biology and evolution · 2019Article
- Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences.Proteomics · 2018Review
- Combining theoretical and experimental data to decipher CFTR 3D structures and functions.Cellular and molecular life sciences : CMLS · 2018Article
- Unique function words characterize genomic proteins.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome.PloS one · 2017Article
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2 authors.
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Abstract
The protein universe corresponds to the set of all proteins found in all organisms. A way to explore it is by taking into account the domain content of the proteins. However, some part of sequences and many entire sequences remain un-annotated despite a converging number of domain families. The un-annotated part of the protein universe is referred to as the dark proteome and remains poorly characterized. In this study, we quantify the amount of foldable domains within the dark proteome by using the hydrophobic cluster analysis methodology. These un-annotated foldable domains were grouped using a combination of remote homology searches and domain annotations, leading to define different levels of darkness. The dark foldable domains were analyzed to understand what make them different from domains stored in databases and thus difficult to annotate. The un-annotated domains of the dark proteome universe display specific features relative to database domains: shorter length, non-canonical content and particular topology in hydrophobic residues, higher propensity for disorder, and a higher energy. These features make them hard to relate to known families. Based on these observations, we emphasize that domain annotation methodologies can still be improved to fully apprehend and decipher the molecular evolution of the protein universe.
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