ArticleJournal of proteome research2019
Blinded Testing of Function Annotation for uPE1 Proteins by I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 23 citations in OpenAlex.
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- Predicting the Structural Impact of Human Alternative Splicing.bioRxiv : the preprint server for biology · 2023Article
- The First Pituitary Proteome Landscape From Matched Anterior and Posterior Lobes for a Better Understanding of the Pituitary Gland.Molecular & cellular proteomics : MCP · 2023Article
- I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nature protocols · 2022Review
- Evolution of Protein Functional Annotation: Text Mining Study.Journal of personalized medicine · 2022Article
- RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control.Cellular and molecular life sciences : CMLS · 2022Article
- Identifying Functions of Proteins in Mice With Functional Embedding Features.Frontiers in genetics · 2022Article
- Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project.Journal of proteome research · 2021Article
- Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students.Database : the journal of biological databases and curation · 2021Article
- Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.Journal of proteome research · 2021Article
- Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years.Molecular & cellular proteomics : MCP · 2021Article
- Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project.Journal of proteome research · 2020Article
- A high-stringency blueprint of the human proteome.Nature communications · 2020Review
- Article
- Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project.Journal of proteome research · 2019Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
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Abstract
In 2018, we reported a hybrid pipeline that predicts protein structures with I-TASSER and function with COFACTOR. I-TASSER/COFACTOR achieved Gene Ontology (GO) high prediction accuracies of Fmax = 0.69 and 0.57 for molecular function (MF) and biological process (BP), respectively, on 100 comprehensively annotated proteins. Now we report blinded analyses of newly annotated proteins in the critical assessment of function annotation (CAFA) three function prediction challenge and in neXtProt. For CAFA3 results released in May 2019, our predictions on 267 and 912 human proteins with newly annotated MF and BP terms achieved Fmax = 0.50 and 0.42, respectively, on "No Knowledge" proteins, and 0.51 and 0.74, respectively, on "Limited Knowledge" proteins. While COFACTOR consistently outperforms simple homology-based analysis, its accuracy still depends on template availability. Meanwhile, in neXtProt 2019-01, 25 proteins acquired new function annotation through literature curation at UniProt/Swiss-Prot. Before the release of these curated results, we submitted to neXtProt blinded predictions of free-text function annotation based on predicted GO terms. For 10 of the 25, a good match of free-text or GO term annotation was obtained. These blind tests represent rigorous assessments of I-TASSER/COFACTOR. neXtProt now provides links to precomputed I-TASSER/COFACTOR predictions for proteins without function annotation to facilitate experimental planning on "dark proteins".
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