ArticleBMC systems biology2014
Improving protein function prediction using domain and protein complexes in PPI networks.
Article in BMC systems biology, 2014. 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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18 citing papers in PubMed.
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- DA-HGL: a domain-augmented heterogeneous graph learning framework for protein function prediction.Briefings in bioinformatics · 2025Article
- Protein function prediction using GO similarity-based heterogeneous network propagation.Scientific reports · 2025Article
- Protein function annotation based on heterogeneous biological networks.BMC bioinformatics · 2022Article
- A tensor-based bi-random walks model for protein function prediction.BMC bioinformatics · 2022Article
- PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms.Frontiers in genetics · 2022Article
- Gene Ontology Capsule GAN: an improved architecture for protein function prediction.PeerJ. Computer science · 2022Article
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- NPF:network propagation for protein function prediction.BMC bioinformatics · 2020Article
- Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning.Briefings in bioinformatics · 2020Article
- Functional expression and impact of testis-specific gene antigen 10 in breast cancer: a combined in vitro and in silico analysis.BioImpacts : BI · 2019Article
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- Harnessing Marine Biocatalytic Reservoirs for Green Chemistry Applications through Metagenomic Technologies.Marine drugs · 2018Review
- Genome-wide characterization and analysis of bHLH transcription factors inActa pharmaceutica Sinica. B · 2018Article
- In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks.BMC systems biology · 2016Article
- An efficient method for protein function annotation based on multilayer protein networks.Human genomics · 2016Article
- Disease Resistance Gene Analogs (RGAs) in Plants.International journal of molecular sciences · 2015Review
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundCharacterization of unknown proteins through computational approaches is one of the most challenging problems in silico biology, which has attracted world-wide interests and great efforts. There have been some computational methods proposed to address this problem, which are either based on homology mapping or in the context of protein interaction networks.
resultsIn this paper, two algorithms are proposed by integrating the protein-protein interaction (PPI) network, proteins' domain information and protein complexes. The one is domain combination similarity (DCS), which combines the domain compositions of both proteins and their neighbors. The other is domain combination similarity in context of protein complexes (DSCP), which extends the protein functional similarity definition of DCS by combining the domain compositions of both proteins and the complexes including them. The new algorithms are tested on networks of the model species of Saccharomyces cerevisiae to predict functions of unknown proteins using cross validations. Comparing with other several existing algorithms, the results have demonstrated the effectiveness of our proposed methods in protein function prediction. Furthermore, the algorithm DSCP using experimental determined complex data is robust when a large percentage of the proteins in the network is unknown, and it outperforms DCS and other several existing algorithms.
conclusionsThe accuracy of predicting protein function can be improved by integrating the protein-protein interaction (PPI) network, proteins' domain information and protein complexes.
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