ArticlePLoS computational biology2013
Comprehensive repertoire of foldable regions within whole genomes.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Impact of GC content on de novo gene birth.Nature communications · 2026Article
- The Analysis ofCurrent issues in molecular biology · 2025Article
- The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation.Genome biology · 2024Article
- Human paraneoplastic antigen Ma2 (PNMA2) forms icosahedral capsids that can be engineered for mRNA delivery.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Digging into the 3D Structure Predictions of AlphaFold2 with Low Confidence: Disorder and Beyond.Biomolecules · 2022Article
- Article
- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Exploring the Peptide Potential of Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.Genome research · 2021Article
- Article
- Protein Corona Composition of Silica Nanoparticles in Complex Media: Nanoparticle Size does not Matter.Nanomaterials (Basel, Switzerland) · 2020Article
- Article
- Discovery and Evolution of New Domains in Yeast Heterochromatin Factor Sir4 and Its Partner Esc1.Genome biology and evolution · 2019Article
- Robustness by intrinsically disordered C-termini and translational readthrough.Nucleic acids research · 2018Article
- Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences.Proteomics · 2018Review
- Article
- Adaptation of mRNA structure to control protein folding.RNA biology · 2017Review
- The Goddard and Saturn Genes Are Essential for Drosophila Male Fertility and May Have Arisen De Novo.Molecular biology and evolution · 2017Article
- Exploring the dark foldable proteome by considering hydrophobic amino acids topology.Scientific reports · 2017Article
- Role of mRNA structure in the control of protein folding.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In order to get a comprehensive repertoire of foldable domains within whole proteomes, including orphan domains, we developed a novel procedure, called SEG-HCA. From only the information of a single amino acid sequence, SEG-HCA automatically delineates segments possessing high densities in hydrophobic clusters, as defined by Hydrophobic Cluster Analysis (HCA). These hydrophobic clusters mainly correspond to regular secondary structures, which together form structured or foldable regions. Genome-wide analyses revealed that SEG-HCA is opposite of disorder predictors, both addressing distinct structural states. Interestingly, there is however an overlap between the two predictions, including small segments of disordered sequences, which undergo coupled folding and binding. SEG-HCA thus gives access to these specific domains, which are generally poorly represented in domain databases. Comparison of the whole set of SEG-HCA predictions with the Conserved Domain Database (CDD) also highlighted a wide proportion of predicted large (length >50 amino acids) segments, which are CDD orphan. These orphan sequences may either correspond to highly divergent members of already known families or belong to new families of domains. Their comprehensive description thus opens new avenues to investigate new functional and/or structural features, which remained so far uncovered. Altogether, the data described here provide new insights into the protein architecture and organization throughout the three kingdoms of life.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.