ArticleProceedings of the National Academy of Sciences of the United States of America2012
Templates are available to model nearly all complexes of structurally characterized proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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96 citing papers in PubMed.
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- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- From In Silico to a Cellular Model: Molecular Docking Approach to Evaluate Antioxidant Bioactive Peptides.Antioxidants (Basel, Switzerland) · 2023Review
- Using PlaPPISite to Predict and Analyze Plant Protein-Protein Interaction Sites.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Dockground resource for protein recognition studies.Protein science : a publication of the Protein Society · 2022Article
- HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry.Bioinformatics (Oxford, England) · 2022Article
- Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants.Protein science : a publication of the Protein Society · 2022Article
- GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.Journal of molecular biology · 2022Article
- Dockground scoring benchmarks for protein docking.Proteins · 2022Article
- Matching protein surface structural patches for high-resolution blind peptide docking.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Improved prediction of protein-protein interactions using AlphaFold2.Nature communications · 2022Article
- Distance-based reconstruction of protein quaternary structures from inter-chain contacts.Proteins · 2022Article
- Protein-protein interaction prediction with deep learning: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- Article
- RR3DD: an RNA global structure-based RNA three-dimensional structural classification database.RNA biology · 2021Article
36 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Traditional approaches to protein-protein docking sample the binding modes with no regard to similar experimentally determined structures (templates) of protein-protein complexes. Emerging template-based docking approaches utilize such similar complexes to determine the docking predictions. The docking problem assumes the knowledge of the participating proteins' structures. Thus, it provides the possibility of aligning the structures of the proteins and the template complexes. The progress in the development of template-based docking and the vast experience in template-based modeling of individual proteins show that, generally, such approaches are more reliable than the free modeling. The key aspect of this modeling paradigm is the availability of the templates. The current common perception is that due to the difficulties in experimental structure determination of protein-protein complexes, the pool of docking templates is insignificant, and thus a broad application of template-based docking is possible only at some future time. The results of our large scale, systematic study show that, surprisingly, in spite of the limited number of protein-protein complexes in the Protein Data Bank, docking templates can be found for complexes representing almost all the known protein-protein interactions, provided the components themselves have a known structure or can be homology-built. About one-third of the templates are of good quality when they are compared to experimental structures in test sets extracted from the Protein Data Bank and would be useful starting points in modeling the complexes. This finding dramatically expands our ability to model protein interactions, and has far-reaching implications for the protein docking field in general.
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