ArticlePloS one2011
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 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
75 citing papers in PubMed.
- A novel method to select Reference Proteomes in UniProt.bioRxiv : the preprint server for biology · 2026Article
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- Structure-informed protein language models are robust predictors for variant effects.Human genetics · 2025Article
- Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes.The EMBO journal · 2024Article
- gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota.Nature biotechnology · 2023Article
- Structure-Informed Protein Language Models are Robust Predictors for Variant Effects.Research square · 2023Article
- On the Origin and Evolution of Microbial Mercury Methylation.Genome biology and evolution · 2023Article
- A general mechanism for transcription bubble nucleation in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists.Genome biology and evolution · 2023Article
- Analysis of CheW-like domains provides insights into organization of prokaryotic chemotaxis systems.Proteins · 2023Article
- MobiDB: 10 years of intrinsically disordered proteins.Nucleic acids research · 2023Article
- Disease association and comparative genomics of compositional bias in human proteins.F1000Research · 2023Article
- Developmental and temporal changes in petunia petal transcriptome reveal scent-repressing plant-specific RING-kinase-WD40 protein.Frontiers in plant science · 2023Article
- Chlorine redox chemistry is widespread in microbiology.The ISME journal · 2023Article
- General strategies for using amino acid sequence data to guide biochemical investigation of protein function.Biochemical Society transactions · 2022Review
- Generalizable strategy to analyze domains in the context of parent protein architecture: A CheW case study.Proteins · 2022Article
- Cross-modality and self-supervised protein embedding for compound-protein affinity and contact prediction.Bioinformatics (Oxford, England) · 2022Article
- Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet.EBioMedicine · 2022Observational
- Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria.Molecular biology and evolution · 2022Article
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15 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. To this end we have developed a set of Representative Proteomes (RPs), each selected from a Representative Proteome Group (RPG) containing similar proteomes calculated based on co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold (CMT) are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements. We find that a CMT of 55% (RP55) most closely follows standard taxonomic classifications. Further analysis of this set reveals that sequence space is reduced by more than 80% relative to UniProtKB, while retaining both sequence diversity (over 95% of InterPro domains) and annotation information (93% of experimentally characterized proteins). All sets can be browsed and are available for sequence similarity searches and download at http://www.proteininformationresource.org/rps, while the set of 637 RPs determined using a 55% CMT are also available for text searches. Potential applications include sequence similarity searches, protein classification and targeted protein annotation and characterization.
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