ArticleBMC research notes2018
Proteome-wide comparison between the amino acid composition of domains and linkers.
Article in BMC research notes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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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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.
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Who cites it
27 citing papers in PubMed.
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- Computational insights into the natural phage endolysin linker landscape.BioData mining · 2026Article
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- Small heat shock protein HSPB5 uses disorder to bind zinc with high affinity.bioRxiv : the preprint server for biology · 2025Article
- Ribosomal expansion segment contributes to translation fidelity via N-terminal processing of ribosomal proteins.Nucleic acids research · 2025Article
- AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations.Protein science : a publication of the Protein Society · 2025Article
- ExploitingJournal of the American Chemical Society · 2025Article
- Site-Specific Histidine Aza-Michael Addition in Proteins Enabled by a Ferritin-Based Metalloenzyme.Journal of the American Chemical Society · 2024Article
- Differential amino acid usage leads to ubiquitous edge effect in proteomes across domains of life that can be explained by amino acid secondary structure propensities.Scientific reports · 2024Article
- Review
- Significance of Histidine Hydrogen-Deuterium Exchange Mass Spectrometry in Protein Structural Biology.Biology · 2024Review
- Amino acid intake strategies define pluripotent cell states.Nature metabolism · 2024Article
- Somatic mutations of MLL4/COMPASS induce cytoplasmic localization providing molecular insight into cancer prognosis and treatment.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Main Factors Shaping Amino Acid Usage Across Evolution.Journal of molecular evolution · 2023Review
- An overview of descriptors to capture protein properties - Tools and perspectives in the context of QSAR modeling.Computational and structural biotechnology journal · 2023Review
- Article
- A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion.Biology · 2022Article
- Exonic splicing code and protein binding sites for calcium.Nucleic acids research · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectiveAmino acid composition is a sequence feature that has been extensively used to characterize proteomes of many species and protein families. Yet the analysis of amino acid composition of protein domains and the linkers connecting them has received less attention. Here, we perform both a comprehensive full-proteome amino acid composition analysis and a similar analysis focusing on domains and linkers, to uncover domain- or linker-specific differential amino acid usage patterns.
resultsThe amino acid composition in the 38 proteomes studied showcase the greater variability found in archaea and bacteria species compared to eukaryotes. When focusing on domains and linkers, we describe the preferential use of polar residues in linkers and hydrophobic residues in domains. To let any user perform this analysis on a given domain (or set of them), we developed a dedicated R script called RACCOON, which can be easily used and can provide interesting insights into the compositional differences between a domain and its surrounding linkers.
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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.