ArticleNucleic acids research2019
INGA 2.0: improving protein function prediction for the dark proteome.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Predicting functions of uncharacterized gene products from microbial communities.Nature biotechnology · 2026Article
- EZpred: improving deep learning-based enzyme function prediction using unlabeled sequence homologs.bioRxiv : the preprint server for biology · 2025Article
- NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations.Genomics, proteomics & bioinformatics · 2023Article
- Machine learning for the identification of respiratory viral attachment machinery from sequences data.PloS one · 2023Article
- I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nature protocols · 2022Review
- A tensor-based bi-random walks model for protein function prediction.BMC bioinformatics · 2022Article
- CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation.PLoS computational biology · 2022Article
- Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect SpeciesBiomolecules · 2022Article
- PANNZER-A practical tool for protein function prediction.Protein science : a publication of the Protein Society · 2022Article
- Semantic similarity and machine learning with ontologies.Briefings in bioinformatics · 2021Review
- NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information.Nucleic acids research · 2021Article
- Review
- NPF:network propagation for protein function prediction.BMC bioinformatics · 2020Article
- Article
- DisProt: intrinsic protein disorder annotation in 2020.Nucleic acids research · 2020Article
- Article
- SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction.Frontiers in bioengineering and biotechnology · 2020Article
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome biology · 2019Article
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2 authors.
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Abstract
Our current knowledge of complex biological systems is stored in a computable form through the Gene Ontology (GO) which provides a comprehensive description of genes function. Prediction of GO terms from the sequence remains, however, a challenging task, which is particularly critical for novel genomes. Here we present INGA 2.0, a new version of the INGA software for protein function prediction. INGA exploits homology, domain architecture, interaction networks and information from the 'dark proteome', like transmembrane and intrinsically disordered regions, to generate a consensus prediction. INGA was ranked in the top ten methods on both CAFA2 and CAFA3 blind tests. The new algorithm can process entire genomes in a few hours or even less when additional input files are provided. The new interface provides a better user experience by integrating filters and widgets to explore the graph structure of the predicted terms. The INGA web server, databases and benchmarking are available from URL: https://inga.bio.unipd.it/.
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