ArticleGenomics, proteomics & bioinformatics2021
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs.
Article in Genomics, proteomics & bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Toward next-generation therapeutic HPV vaccines: A review on expanding the antigen repertoire and an integrated bioinformatics selection framework.Human vaccines & immunotherapeutics · 2026Review
- Accurate proteome-wide prediction of enzymes and catalytic sites using graph deep learning and protein language model.GigaScience · 2026Article
- Machine Learning for Protein Function Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Residual host cell proteins: sources, properties, detection methods and data acquisition modes.Frontiers in microbiology · 2025Review
- BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.Nucleic acids research · 2024Article
- NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations.Genomics, proteomics & bioinformatics · 2023Article
- Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.FEMS microbiology reviews · 2023Review
- An informatic workflow for the enhanced annotation of excretory/secretory proteins ofComputational and structural biotechnology journal · 2023Article
- TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.Genomics, proteomics & bioinformatics · 2022Article
- EnsembleFam: towards more accurate protein family prediction in the twilight zone.BMC bioinformatics · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Genome-Wide Identification and Analysis of NAC Transcription Factor Family in Two Diploid Wild Relatives of Cultivated Sweet Potato Uncovers Potential NAC Genes Related to Drought Tolerance.Frontiers in genetics · 2021Article
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Authors and funding
9 authors.
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Abstract
The number of available protein sequences in public databases is increasing exponentially. However, a significant percentage of these sequences lack functional annotation, which is essential for the understanding of how biological systems operate. Here, we propose a novel method, Quantitative Annotation of Unknown STructure (QAUST), to infer protein functions, specifically Gene Ontology (GO) terms and Enzyme Commission (EC) numbers. QAUST uses three sources of information: structure information encoded by global and local structure similarity search, biological network information inferred by protein-protein interaction data, and sequence information extracted from functionally discriminative sequence motifs. These three pieces of information are combined by consensus averaging to make the final prediction. Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation (CAFA) benchmark set. The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading. We further demonstrate that a previously unknown function of human tripartite motif-containing 22 (TRIM22) protein predicted by QAUST can be experimentally validated.
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