ReviewProteomics2018
Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences.
Review in Proteomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Special Issue "Molecular Dynamics Simulations and Structural Analysis of Protein Domains (2nd Edition)".International journal of molecular sciences · 2026Article
- Impact of GC content on de novo gene birth.Nature communications · 2026Article
- SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Special Issue: "Molecular Dynamics Simulations and Structural Analysis of Protein Domains".International journal of molecular sciences · 2024Article
- Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features.Nature communications · 2024Article
- Assessment of Disordered Linker Predictions in the CAID2 Experiment.Biomolecules · 2024Article
- The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data.Biochemistry and biophysics reports · 2023Article
- Hydrophobicity-Driven Increases in Editing in Mitochondrial mRNAs during the Evolution of Kinetoplastids.Molecular biology and evolution · 2023Article
- Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes.Nature communications · 2022Article
- Digging into the 3D Structure Predictions of AlphaFold2 with Low Confidence: Disorder and Beyond.Biomolecules · 2022Article
- A New Gene Family Diagnostic for Intracellular Biomineralization of Amorphous Ca Carbonates by Cyanobacteria.Genome biology and evolution · 2022Article
- Predicting Protein Conformational Disorder and Disordered Binding Sites.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Deep learning in prediction of intrinsic disorder in proteins.Computational and structural biotechnology journal · 2022Review
- Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.Genome research · 2021Article
- ProteinTools: a toolkit to analyze protein structures.Nucleic acids research · 2021Article
- The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine.Molecular cell · 2020Article
- Biochemical characterization of a glycosyltransferase Gtf3 from3 Biotech · 2020Article
- Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling.Molecular cell · 2020Article
- Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates.Aging · 2020Article
- Rickettsia Sca2 Recruits Two Actin Subunits for Nucleation but Lacks WH2 Domains.Biophysical journal · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hydrophobic cluster analysis (HCA) is an original approach for protein sequence analysis, which provides access to the foldable repertoire of the protein universe, including yet unannotated protein segments ("dark proteome"). Foldable segments correspond to ordered regions, as well as to intrinsically disordered regions (IDRs) undergoing disorder to order transitions. In this review, how HCA can be used to give insight into this last category of foldable segments is illustrated, with examples matching known 3D structures. After reviewing the HCA principles, examples of short foldable segments are given, which often contain short linear motifs, typically matching hydrophobic clusters. These segments become ordered upon contact with partners, with secondary structure preferences generally corresponding to those observed in the 3D structures within the complexes. Such small foldable segments are sometimes larger than the segments of known 3D structures, including flanking hydrophobic clusters that may be critical for interaction specificity or regulation, as well as intervening sequences allowing fuzziness. Cases of larger conditionally disordered domains are also presented, with lower density in hydrophobic clusters than well-folded globular domains or with exposed hydrophobic patches, which are stabilized by interaction with partners.
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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.