ArticleJournal of the Royal Society, Interface2006
Modelling protein-protein interaction networks via a stickiness index.
Article in Journal of the Royal Society, Interface, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Machine Learning and Deep Learning Frameworks for Human-Virus Protein-Protein Interaction Prediction: Emerging Architectures, Methods, Benchmarks, and Challenges.International journal of molecular sciences · 2026Review
- Connectivity of Random Geometric Hypergraphs.Entropy (Basel, Switzerland) · 2023Article
- Metrics for network comparison using egonet feature distributions.Scientific reports · 2023Article
- Chromatin network markers of leukemia.Bioinformatics (Oxford, England) · 2020Article
- NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families.PloS one · 2020Article
- Towards a data-integrated cell.Nature communications · 2019Article
- A comprehensive evaluation of module detection methods for gene expression data.Nature communications · 2018Article
- Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins.Genome biology and evolution · 2017Article
- Proper evaluation of alignment-free network comparison methods.Bioinformatics (Oxford, England) · 2015Article
- Revisiting topological properties and models of protein-protein interaction networks from the perspective of dataset evolution.IET systems biology · 2015Article
- Revealing the hidden language of complex networks.Scientific reports · 2014Article
- Modelling the yeast interactome.Scientific reports · 2014Article
- A low dimensional approach on network characterization.PloS one · 2014Article
- A comparative study of theoretical graph models for characterizing structural networks of human brain.International journal of biomedical imaging · 2013Article
- t-LSE: a novel robust geometric approach for modeling protein-protein interaction networks.PloS one · 2013Article
- Article
- Viruses and interactomes in translation.Molecular & cellular proteomics : MCP · 2012Article
- Assessing and predicting protein interactions by combining manifold embedding with multiple information integration.BMC bioinformatics · 2012Article
- GraphCrunch 2: Software tool for network modeling, alignment and clustering.BMC bioinformatics · 2011Article
- How threshold behaviour affects the use of subgraphs for network comparison.Bioinformatics (Oxford, England) · 2010Article
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Authors and funding
2 authors.
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Abstract
What type of connectivity structure are we seeing in protein-protein interaction networks? A number of random graph models have been mooted. After fitting model parameters to real data, the models can be judged by their success in reproducing key network properties. Here, we propose a very simple random graph model that inserts a connection according to the degree, or 'stickiness', of the two proteins involved. This model can be regarded as a testable distillation of more sophisticated versions that attempt to account for the presence of interaction surfaces or binding domains. By computing a range of network similarity measures, including relative graphlet frequency distance, we find that our model outperforms other random graph classes. In particular, we show that given the underlying degree information, fitting a stickiness model produces better results than simply choosing a degree-matching graph uniformly at random. Therefore, the results lend support to the basic modelling methodology.
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