ArticleBioinformatics (Oxford, England)2016
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- How to approach machine learning-based prediction of drug/compound-target interactions.Journal of cheminformatics · 2023Article
- ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations.Computational and structural biotechnology journal · 2023Article
- An OFrontiers in microbiology · 2023Article
- Clinical and bi-genomic DNA findings of patients suspected to have mitochondrial diseases.Frontiers in genetics · 2023Article
- An 85-amino-acid polypeptide fromAsian biomedicine : research, reviews and news · 2022Article
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- Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases.PLoS computational biology · 2021Article
- Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome.mSystems · 2021Article
- Assessment of a complete and classified platelet proteome from genome-wide transcripts of human platelets and megakaryocytes covering platelet functions.Scientific reports · 2021Article
- Self-assembled fibrinogen-fibronectin hybrid protein nanofibers with medium-sensitive stability.RSC advances · 2021Article
- Inhibiting Sialidase-Induced TGF-The Journal of pharmacology and experimental therapeutics · 2021Article
- DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations.Chemical science · 2020Article
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- DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks.Scientific reports · 2019Article
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7 authors.
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Abstract
motivationSimilarity-based methods have been widely used in order to infer the properties of genes and gene products containing little or no experimental annotation. New approaches that overcome the limitations of methods that rely solely upon sequence similarity are attracting increased attention. One of these novel approaches is to use the organization of the structural domains in proteins.
resultsWe propose a method for the automatic annotation of protein sequences in the UniProt Knowledgebase (UniProtKB) by comparing their domain architectures, classifying proteins based on the similarities and propagating functional annotation. The performance of this method was measured through a cross-validation analysis using the Gene Ontology (GO) annotation of a sub-set of UniProtKB/Swiss-Prot. The results demonstrate the effectiveness of this approach in detecting functional similarity with an average F-score: 0.85. We applied the method on nearly 55.3 million uncharacterized proteins in UniProtKB/TrEMBL resulted in 44 818 178 GO term predictions for 12 172 114 proteins. 22% of these predictions were for 2 812 016 previously non-annotated protein entries indicating the significance of the value added by this approach. AVAILABILITY AND IMPLEMENTATION: The results of the method are available at: ftp://ftp.ebi.ac.uk/pub/contrib/martin/DAAC/ CONTACT: tdogan@ebi.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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