ArticleJournal of molecular biology2008
Architectures and functional coverage of protein-protein interfaces.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function.Journal of molecular biology · 2025Review
- Conformational diversity and protein-protein interfaces in drug repurposing in Ras signaling pathway.Scientific reports · 2024Article
- Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains.Protein science : a publication of the Protein Society · 2022Article
- Structural motifs in protein cores and at protein-protein interfaces are different.Protein science : a publication of the Protein Society · 2021Article
- Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Targeting Difficult Protein-Protein Interactions with Plain and General Computational Approaches.Molecules (Basel, Switzerland) · 2018Review
- Dockground: A comprehensive data resource for modeling of protein complexes.Protein science : a publication of the Protein Society · 2018Article
- Protein structural motifs in prediction and design.Current opinion in structural biology · 2017Review
- Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information.Methods in molecular biology (Clifton, N.J.) · 2017Article
- PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.Acta crystallographica. Section D, Structural biology · 2016Article
- Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.Biophysical journal · 2015Article
- Structural templates for comparative protein docking.Proteins · 2015Article
- Decomposing the space of protein quaternary structures with the interface fragment pair library.BMC bioinformatics · 2015Article
- Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.Nucleic acids research · 2015Article
- Modeling protein assemblies in the proteome.Molecular & cellular proteomics : MCP · 2014Article
- The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer.PLoS computational biology · 2014Article
- Non-redundant unique interface structures as templates for modeling protein interactions.PloS one · 2014Article
- Article
- Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale.Journal of proteome research · 2013Article
- Toward a "structural BLAST": using structural relationships to infer function.Protein science : a publication of the Protein Society · 2013Review
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Authors and funding
5 authors.
Funding
Abstract
The diverse range of cellular functions is performed by a limited number of protein folds existing in nature. One may similarly expect that cellular functional diversity would be covered by a limited number of protein-protein interface architectures. Here, we present 8205 interface clusters, each representing a unique interface architecture. This data set of protein-protein interfaces is analyzed and compared with older data sets. We observe that the number of both biological and crystal interfaces increases significantly compared to the number of Protein Data Bank entries. Furthermore, we find that the number of distinct interface architectures grows at a much faster rate than the number of folds and is yet to level off. We further analyze the growth trend of the functional coverage by constructing functional interaction networks from interfaces. The functional coverage is also found to steadily increase. Interestingly, we also observe that despite the diversity of interface architectures, some are more favorable and frequently used, and of particular interest, are the ones that are also preferred in single chains.
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