ArticleProtein science : a publication of the Protein Society2006
Finding biologically relevant protein domain interactions: conserved binding mode analysis.
Article in Protein science : a publication of the Protein Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Computational Methods and Deep Learning for Elucidating Protein Interaction Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Genome-wide analysis of transmembrane 9 superfamily genes in wheat (Frontiers in plant science · 2023Article
- Phosphatase POPX2 interferes with cell cycle by interacting with Chk1.Cell cycle (Georgetown, Tex.) · 2020Article
- Building Bridges Between Structural and Network-Based Systems Biology.Molecular biotechnology · 2019Review
- Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.Nucleic acids research · 2019Article
- Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family.Scientific reports · 2017Article
- Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Progress and challenges in predicting protein interfaces.Briefings in bioinformatics · 2016Review
- Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.Biophysical journal · 2015Article
- A structure-based classification and analysis of protein domain family binding sites and their interactions.Biology · 2015Article
- K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores.Journal of clinical bioinformatics · 2015Article
- On the role of physics and evolution in dictating protein structure and function.Israel journal of chemistry · 2014Article
- 3did: a catalog of domain-based interactions of known three-dimensional structure.Nucleic acids research · 2014Article
- Protein-protein interaction networks (PPI) and complex diseases.Gastroenterology and hepatology from bed to bench · 2014Review
- Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization.Progress in molecular biology and translational science · 2013Review
- Article
- Chapter 4: Protein interactions and disease.PLoS computational biology · 2012Article
- Alternative protein-protein interfaces are frequent exceptions.PLoS computational biology · 2012Article
- Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization.Physical biology · 2011Review
- DOMINE: a comprehensive collection of known and predicted domain-domain interactions.Nucleic acids research · 2011Article
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3 authors.
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Abstract
Proteins evolved through the shuffling of functional domains, and therefore, the same domain can be found in different proteins and species. Interactions between such conserved domains often involve specific, well-determined binding surfaces reflecting their important biological role in a cell. To find biologically relevant interactions we developed a method of systematically comparing and classifying protein domain interactions from the structural data. As a result, a set of conserved binding modes (CBMs) was created using the atomic detail of structure alignment data and the protein domain classification of the Conserved Domain Database. A conserved binding mode is inferred when different members of interacting domain families dock in the same way, such that their structural complexes superimpose well. Such domain interactions with recurring structural themes have greater significance to be biologically relevant, unlike spurious crystal packing interactions. Consequently, this study gives lower and upper bounds on the number of different types of interacting domain pairs in the structure database on the order of 1000-2000. We use CBMs to create domain interaction networks, which highlight functionally significant connections by avoiding many infrequent links between highly connected nodes. The CBMs also constitute a library of docking templates that may be used in molecular modeling to infer the characteristics of an unknown binding surface, just as conserved domains may be used to infer the structure of an unknown protein. The method's ability to sort through and classify large numbers of putative interacting domain pairs is demonstrated on the oligomeric interactions of globins.
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