ArticleScientific reports2016
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 62 citations in OpenAlex.
- Centipede Polypeptide Affects the Inflammatory Reaction and Ferroptosis of Liver Cancer Cells Through the p53/TRAIL Pathway.Journal of cellular and molecular medicine · 2025Article
- Peptide-Based Strategies AgainstPharmaceuticals (Basel, Switzerland) · 2025Review
- Flexible Docking of Cyclic Peptides to Proteins Using CABS-dock.Journal of chemical theory and computation · 2025Article
- Mechanistic Role of the Mdm2/MdmX Lid Domain in Regulating Their Interactions with p53.Biomolecules · 2025Review
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Exploring protein functions from structural flexibility using CABS-flex modeling.Protein science : a publication of the Protein Society · 2024Review
- An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale.Journal of chemical theory and computation · 2024Article
- Article
- Molecular Docking and Molecular Dynamics Simulations in Related toTropical medicine and infectious disease · 2023Review
- Integrative modeling of diverse protein-peptide systems using CABS-dock.PLoS computational biology · 2023Article
- Multiscale Modeling of Amyloid Fibrils Formed by Aggregating Peptides Derived from the Amyloidogenic Fragment of the A-Chain of Insulin.International journal of molecular sciences · 2021Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Molecular Dynamics Scoring of Protein-Peptide Models Derived from Coarse-Grained Docking.Molecules (Basel, Switzerland) · 2021Article
- Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement.Briefings in bioinformatics · 2021Article
- Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering.Frontiers in molecular biosciences · 2021Review
- 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
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Probing the local conformational flexibility in receptor recognition: mechanistic insight from an atomic-scale investigation.RSC advances · 2019Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the CABS-dock method for flexible protein-peptide docking that enables large-scale rearrangements of the protein chain. In this study, we use CABS-dock to investigate the binding of the p53-MDM2 complex, an element of the cell cycle regulation system crucial for anti-cancer drug design. Experimental data suggest that p53-MDM2 binding is affected by significant rearrangements of a lid region - the N-terminal highly flexible MDM2 fragment; however, the details are not clear. The large size of the highly flexible MDM2 fragments makes p53-MDM2 intractable for exhaustive binding dynamics studies using atomistic models. We performed extensive dynamics simulations using the CABS-dock method, including large-scale structural rearrangements of MDM2 flexible regions. Without a priori knowledge of the p53 peptide structure or its binding site, we obtained near-native models of the p53-MDM2 complex. The simulation results match well the experimental data and provide new insights into the possible role of the lid fragment in p53 binding. The presented case study demonstrates that CABS-dock methodology opens up new opportunities for protein-peptide docking with large-scale changes of the protein receptor structure.
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