ArticleJournal of proteome research2013
Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale.
Article in Journal of proteome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 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
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
- PBX3 Promotes Tumor Growth and Angiogenesis via Activation of AT1R/VEGFR2 Pathway in Papillary Thyroid Carcinoma.BioMed research international · 2020Article
- Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins.Scientific reports · 2017Article
- Template-based protein-protein docking exploiting pairwise interfacial residue restraints.Briefings in bioinformatics · 2017Article
- Modeling of RAS complexes supports roles in cancer for less studied partners.BMC biophysics · 2017Article
- 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
- DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.Nucleic acids research · 2016Article
- PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.Acta crystallographica. Section D, Structural biology · 2016Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Evolutionary Conserved Positions Define Protein Conformational Diversity.PLoS computational biology · 2016Article
- CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state.Database : the journal of biological databases and curation · 2016Article
- Article
- Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP.Biophysical journal · 2015Article
- The structural basis for cancer treatment decisions.Oncotarget · 2014Review
- PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.Nucleic acids research · 2014Article
- BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures.Journal of chemical information and modeling · 2014Article
- 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
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Authors and funding
4 authors.
Funding
Abstract
Cellular functions are performed through protein-protein interactions; therefore, identification of these interactions is crucial for understanding biological processes. Recent studies suggest that knowledge-based approaches are more useful than "blind" docking for modeling at large scales. However, a caveat of knowledge-based approaches is that they treat molecules as rigid structures. The Protein Data Bank (PDB) offers a wealth of conformations. Here, we exploited an ensemble of the conformations in predictions by a knowledge-based method, PRISM. We tested "difficult" cases in a docking-benchmark data set, where the unbound and bound protein forms are structurally different. Considering alternative conformations for each protein, the percentage of successfully predicted interactions increased from ~26 to 66%, and 57% of the interactions were successfully predicted in an "unbiased" scenario, in which data related to the bound forms were not utilized. If the appropriate conformation, or relevant template interface, is unavailable in the PDB, PRISM could not predict the interaction successfully. The pace of the growth of the PDB promises a rapid increase of ensemble conformations emphasizing the merit of such knowledge-based ensemble strategies for higher success rates in protein-protein interaction predictions on an interactome scale. We constructed the structural network of ERK interacting proteins as a case study.
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