ArticleBioinformatics (Oxford, England)2012
Protein domain recurrence and order can enhance prediction of protein functions.
Article in Bioinformatics (Oxford, England), 2012. 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.
- Predicting Protein Functions with Function-Aware Domain Embeddings Using Domain-PFP.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Domain-PFP allows protein function prediction using function-aware domain embedding representations.Communications biology · 2023Article
- Domain-PFP: Protein Function Prediction Using Function-Aware Domain Embedding Representations.bioRxiv : the preprint server for biology · 2023Article
- FAS: assessing the similarity between proteins using multi-layered feature architectures.Bioinformatics (Oxford, England) · 2023Article
- Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.Bioinformatics (Oxford, England) · 2019Article
- Missing gene identification using functional coherence scores.Scientific reports · 2016Article
- UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.Bioinformatics (Oxford, England) · 2016Article
- CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.Bioinformatics (Oxford, England) · 2016Article
- PatchSurfers: Two methods for local molecular property-based binding ligand prediction.Methods (San Diego, Calif.) · 2016Article
- Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.F1000Research · 2016Article
- Domain similarity based orthology detection.BMC bioinformatics · 2015Article
- DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.BMC bioinformatics · 2015Article
- Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.PLoS computational biology · 2014Article
- LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone.BMC bioinformatics · 2014Article
- Computational prediction of protein function based on weighted mapping of domains and GO terms.BioMed research international · 2014Article
- Recent advances in computational methods for nuclear magnetic resonance data processing.Genomics, proteomics & bioinformatics · 2013Review
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5 authors.
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Abstract
motivationBurgeoning sequencing technologies have generated massive amounts of genomic and proteomic data. Annotating the functions of proteins identified in this data has become a big and crucial problem. Various computational methods have been developed to infer the protein functions based on either the sequences or domains of proteins. The existing methods, however, ignore the recurrence and the order of the protein domains in this function inference.
resultsWe developed two new methods to infer protein functions based on protein domain recurrence and domain order. Our first method, DRDO, calculates the posterior probability of the Gene Ontology terms based on domain recurrence and domain order information, whereas our second method, DRDO-NB, relies on the naïve Bayes methodology using the same domain architecture information. Our large-scale benchmark comparisons show strong improvements in the accuracy of the protein function inference achieved by our new methods, demonstrating that domain recurrence and order can provide important information for inference of protein functions. AVAILABILITY: The new models are provided as open source programs at http://sfb.kaust.edu.sa/Pages/Software.aspx. CONTACT: dkihara@cs.purdue.edu, xin.gao@kaust.edu.sa SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.
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