ArticleNucleic acids research2012
CombFunc: predicting protein function using heterogeneous data sources.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- EZpred: improving deep learning-based enzyme function prediction using unlabeled sequence homologs.bioRxiv : the preprint server for biology · 2025Article
- ICoN: integration using co-attention across biological networks.Bioinformatics advances · 2025Article
- A Survey of Biological Function Prediction Methods with Focus on Natural Language Processing (NLP) and Large Language Models (LLM).Methods in molecular biology (Clifton, N.J.) · 2025Article
- A large-scale assessment of sequence database search tools for homology-based protein function prediction.Briefings in bioinformatics · 2024Article
- Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review.Molecules (Basel, Switzerland) · 2023Review
- Structure-based protein function prediction using graph convolutional networks.Nature communications · 2021Article
- Hierarchical Microbial Functions Prediction by Graph Aggregated Embedding.Frontiers in genetics · 2020Article
- Exploring the computational methods for protein-ligand binding site prediction.Computational and structural biotechnology journal · 2020Review
- Predicting Sequence Features, Function, and Structure of Proteins Using MESSA.Current protocols in bioinformatics · 2019Article
- UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction.BMC bioinformatics · 2019Article
- Environmental conditions shape the nature of a minimal bacterial genome.Nature communications · 2019Article
- NetGO: improving large-scale protein function prediction with massive network information.Nucleic acids research · 2019Article
- DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks.Scientific reports · 2019Article
- Improving protein function prediction using protein sequence and GO-term similarities.Bioinformatics (Oxford, England) · 2019Article
- Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion.ACS omega · 2019Article
- deepNF: deep network fusion for protein function prediction.Bioinformatics (Oxford, England) · 2018Article
- MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.Journal of molecular biology · 2018Article
- DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.Bioinformatics (Oxford, England) · 2018Article
- Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate.International journal of molecular sciences · 2018Article
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3 authors.
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Abstract
Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions. CombFunc incorporates ConFunc, our existing function prediction method, with other approaches for function prediction that use protein sequence, gene expression and protein-protein interaction data. In benchmarking on a set of 1686 proteins CombFunc obtains precision and recall of 0.71 and 0.64 respectively for gene ontology molecular function terms. For biological process GO terms precision of 0.74 and recall of 0.41 is obtained. CombFunc is available at http://www.sbg.bio.ic.ac.uk/combfunc.
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