ArticleBiomedical engineering online2017
Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif.
Article in Biomedical engineering online, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Flexible Docking of Cyclic Peptides to Proteins Using CABS-dock.Journal of chemical theory and computation · 2025Article
- Computer- and NMR-Aided Design of Small-Molecule Inhibitors of the Hub1 Protein.Molecules (Basel, Switzerland) · 2022Article
- Anti-breast cancer synthetic peptides derived from the Anabas testudineus skin mucus fractions.Scientific reports · 2021Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement.Briefings in bioinformatics · 2021Article
- Flexible docking of peptides to proteins using CABS-dock.Protein science : a publication of the Protein Society · 2020Article
- Protein-peptide docking using CABS-dock and contact information.Briefings in bioinformatics · 2019Article
- CABS-dock standalone: a toolbox for flexible protein-peptide docking.Bioinformatics (Oxford, England) · 2019Article
- Probing the local conformational flexibility in receptor recognition: mechanistic insight from an atomic-scale investigation.RSC advances · 2019Article
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
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Authors and funding
5 authors.
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Abstract
backgroundMany protein-protein interactions are mediated by a short linear motif. Usually, amino acid sequences of those motifs are known or can be predicted. It is much harder to experimentally characterize or predict their structure in the bound form. In this work, we test a possibility of using flexible docking of a short linear motif to predict the interaction interface of the EphB4-EphrinB2 complex (a system extensively studied for its significance in tumor progression).
methodsIn the modeling, we only use knowledge about the motif sequence and experimental structures of EphB4-EphrinB2 complex partners. The proposed protocol enables efficient modeling of significant conformational changes in the short linear motif fragment during molecular docking simulation. For the docking simulations, we use the CABS-dock method for docking fully flexible peptides to flexible protein receptors (available as a server at http://biocomp.chem.uw.edu.pl/CABSdock/ ). Based on the docking result, the protein-protein complex is reconstructed and refined.
resultsUsing this novel protocol, we obtained an accurate EphB4-EphrinB2 interaction model.
conclusionsThe results show that the CABS-dock method may be useful as the primary docking tool in specific protein-protein docking cases similar to EphB4-EphrinB2 complex-that is, where a short linear motif fragment can be identified.
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