ArticleNucleic acids research2015
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- A multi-scale biological network framework for discovering MiRNA-Disease associations.Frontiers in bioinformatics · 2026Article
- Machine Learning for Protein Function Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- A Comprehensive Review on Machine Learning Techniques for Protein Family Prediction.The protein journal · 2024Review
- AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding.Genome biology · 2024Article
- Article
- A tensor-based bi-random walks model for protein function prediction.BMC bioinformatics · 2022Article
- EnsembleFam: towards more accurate protein family prediction in the twilight zone.BMC bioinformatics · 2022Article
- PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms.Frontiers in genetics · 2022Article
- QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs.Genomics, proteomics & bioinformatics · 2021Article
- Augmented sequence features and subcellular localization for functional characterization of unknown protein sequences.Medical & biological engineering & computing · 2021Article
- Protein function prediction with gene ontology: from traditional to deep learning models.PeerJ · 2021Article
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- NPF:network propagation for protein function prediction.BMC bioinformatics · 2020Article
- Graph2GO: a multi-modal attributed network embedding method for inferring protein functions.GigaScience · 2020Article
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.Future generations computer systems : FGCS · 2019Article
- UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction.BMC bioinformatics · 2019Article
- INGA 2.0: improving protein function prediction for the dark proteome.Nucleic acids research · 2019Article
- NetGO: improving large-scale protein function prediction with massive network information.Nucleic acids research · 2019Article
- Article
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5 authors.
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Abstract
Identifying protein functions can be useful for numerous applications in biology. The prediction of gene ontology (GO) functional terms from sequence remains however a challenging task, as shown by the recent CAFA experiments. Here we present INGA, a web server developed to predict protein function from a combination of three orthogonal approaches. Sequence similarity and domain architecture searches are combined with protein-protein interaction network data to derive consensus predictions for GO terms using functional enrichment. The INGA server can be queried both programmatically through RESTful services and through a web interface designed for usability. The latter provides output supporting the GO term predictions with the annotating sequences. INGA is validated on the CAFA-1 data set and was recently shown to perform consistently well in the CAFA-2 blind test. The INGA web server is available from URL: http://protein.bio.unipd.it/inga.
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