ArticleNucleic acids research2017
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 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
15 citing papers in PubMed, 45 citations in OpenAlex.
- DRED: A Comprehensive Database of Genes Related to Repeat Expansion Diseases.Genomics, proteomics & bioinformatics · 2024Article
- ScrepYard: An online resource for disulfide-stabilized tandem repeat peptides.Protein science : a publication of the Protein Society · 2023Article
- TReSR: A PCR-compatible DNA sequence design method for engineering proteins containing tandem repeats.PloS one · 2023Article
- Pfam: The protein families database in 2021.Nucleic acids research · 2021Article
- Amino acid homorepeats in proteins.Nature reviews. Chemistry · 2020Review
- Self-analysis of repeat proteins reveals evolutionarily conserved patterns.BMC bioinformatics · 2020Article
- Article
- MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudosymmetries.Journal of molecular biology · 2020Article
- Large Ankyrin repeat proteins are formed with similar and energetically favorable units.PloS one · 2020Article
- PRIGSA2: Improved version of protein repeat identification by graph spectral analysis.Journal of biosciences · 2020Article
- Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.Nucleic acids research · 2019Review
- INGA 2.0: improving protein function prediction for the dark proteome.Nucleic acids research · 2019Article
- Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.PLoS computational biology · 2019Article
- Systematic mapping of free energy landscapes of a growing filamin domain during biosynthesis.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.Nucleic acids research · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 3 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity.
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.