ArticleProteins2013
Global and local structural similarity in protein-protein complexes: implications for template-based docking.
Article in Proteins, 2013. 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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Who cites it
18 citing papers in PubMed.
- Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.RSC chemical biology · 2023Review
- Toward Characterising the Cellular 3D-Proteome.Frontiers in bioinformatics · 2021Article
- How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking.Proteins · 2020Article
- Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking.Journal of computer-aided molecular design · 2018Article
- A Novel Geometry-Based Approach to Infer Protein Interface Similarity.Scientific reports · 2018Article
- Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.Proteins · 2018Article
- Dockground: A comprehensive data resource for modeling of protein complexes.Protein science : a publication of the Protein Society · 2018Article
- Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks.BMC bioinformatics · 2017Article
- Template-based protein-protein docking exploiting pairwise interfacial residue restraints.Briefings in bioinformatics · 2017Article
- HOMCOS: an updated server to search and model complex 3D structures.Journal of structural and functional genomics · 2016Article
- Template-Based Modeling of Protein-RNA Interactions.PLoS computational biology · 2016Article
- Modeling and fitting protein-protein complexes to predict change of binding energy.Scientific reports · 2016Article
- Structural templates for comparative protein docking.Proteins · 2015Article
- Article
- Protein-protein docking: from interaction to interactome.Biophysical journal · 2014Review
- PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.Nucleic acids research · 2014Article
- Template-based structure modeling of protein-protein interactions.Current opinion in structural biology · 2014Review
- Non-redundant unique interface structures as templates for modeling protein interactions.PloS one · 2014Article
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2 authors.
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Abstract
The increasing amount of structural information on protein-protein interactions makes it possible to predict the structure of protein-protein complexes by comparison/alignment of the interacting proteins to the ones in cocrystallized complexes. In the predictions based on structure similarity, the template search is performed by structural alignment of the target interactors with the entire structures or with the interface only of the subunits in cocrystallized complexes. This study investigates the scope of the structural similarity that facilitates the detection of a broad range of templates significantly divergent from the targets. The analysis of the target-template similarity is based on models of protein-protein complexes in a large representative set of heterodimers. The similarity of the biological and crystal packing interfaces, dissimilar interface structural motifs in overall similar structures, interface similarity to the full structure, and local similarity away from the interface were analyzed. The structural similarity at the protein-protein interfaces only was observed in ~25% of target-template pairs with sequence identity <20% and primarily homodimeric templates. For ~50% of the target-template pairs, the similarity at the interface was accompanied by the similarity of the whole structure. However, the structural similarity at the interfaces was still stronger than that of the noninterface parts. The study provides insights into structural and functional diversity of protein-protein complexes, and relative performance of the interface and full structure alignment in docking.
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