ArticleNucleic acids research2017
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- On the state of protein function prediction: a report on the fourth CAFA challenge.bioRxiv : the preprint server for biology · 2026Article
- Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective.Applied biochemistry and biotechnology · 2024Review
- Regulatory mechanisms of dopamine metabolism in a marineSynthetic and systems biotechnology · 2024Article
- Prevalence and transmission risk of colistin and multidrug resistance in long-distance coastal aquaculture.ISME communications · 2023Article
- Alone and together: current approaches to targeting glutaminase enzymes as part of anti-cancer therapies.Future drug discovery · 2023Review
- Genome-Scale Modeling and Systems Metabolic Engineering of Vibrio natriegens for the Production of 1,3-Propanediol.Methods in molecular biology (Clifton, N.J.) · 2023Article
- PANNZER-A practical tool for protein function prediction.Protein science : a publication of the Protein Society · 2022Article
- BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation.Nucleic acids research · 2021Article
- BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics.BMC bioinformatics · 2020Article
- Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito.BMC bioinformatics · 2020Article
- Glycogen storage diseases: Twenty-seven new variants in a cohort of 125 patients.Molecular genetics & genomic medicine · 2019Article
- NetGO: improving large-scale protein function prediction with massive network information.Nucleic acids research · 2019Article
- Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion.ACS omega · 2019Article
- MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.Journal of molecular biology · 2018Article
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3 authors.
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Abstract
BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3.
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