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Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction

https://doi.org/10.1038/srep37532
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Computational studies and peptidomimetic design for the human p53–MDM2 complex
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DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility
inferredcites →https://doi.org/10.1002/prot.22716openalex-snapshot
Sub-angstrom modeling of complexes between flexible peptides and globular proteins
inferredcites →https://doi.org/10.1002/prot.24852openalex-snapshot
Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics
inferredcites →https://doi.org/10.1006/jmbi.1997.1078openalex-snapshot
Molecular characterization of the hdm2-p53 interaction 1 1Edited by J. Karn
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Case Study: Discovery of Inhibitors of the MDM2–p53 Protein-Protein Interaction
inferredcites →https://doi.org/10.1007/978-1-4939-6798-8_6openalex-snapshot
Highly Flexible Protein-Peptide Docking Using CABS-Dock
inferredcites →https://doi.org/10.1016/j.bpj.2014.04.022openalex-snapshot
Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors
inferredcites →https://doi.org/10.1016/j.drudis.2014.10.003openalex-snapshot
Peptide therapeutics: current status and future directions
inferredcites →https://doi.org/10.1016/j.jmb.2005.05.010openalex-snapshot
Structure of Free MDM2 N-terminal Domain Reveals Conformational Adjustments that Accompany p53-binding
inferredcites →https://doi.org/10.1016/j.jmgm.2013.10.005openalex-snapshot
Molecular dynamics simulations studies and free energy analysis on inhibitors of MDM2–p53 interaction
inferredcites →https://doi.org/10.1016/j.str.2013.09.006openalex-snapshot
Transient Protein States in Designing Inhibitors of the MDM2-p53 Interaction
inferredcites →https://doi.org/10.1016/j.str.2015.05.021openalex-snapshot
Fully Blind Peptide-Protein Docking with pepATTRACT
inferredcites →https://doi.org/10.1016/j.ymeth.2015.07.004openalex-snapshot
Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking
inferredcites →https://doi.org/10.1021/acs.chemrev.6b00163openalex-snapshot
Coarse-Grained Protein Models and Their Applications
inferredcites →https://doi.org/10.1021/acs.jpcb.5b11162openalex-snapshot
Recognition Dynamics of p53 and MDM2: Implications for Peptide Design
inferredcites →https://doi.org/10.1021/ct4009238openalex-snapshot
Mechanism of Stapled Peptide Binding to MDM2: Possible Consequences for Peptide Design
inferredcites →https://doi.org/10.1021/ct500287copenalex-snapshot
Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations
inferredcites →https://doi.org/10.1021/ja203275fopenalex-snapshot
Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation–Condensation to Framework Mechanism
inferredcites →https://doi.org/10.1021/ja301255nopenalex-snapshot
Interrogation of MDM2 Phosphorylation in p53 Activation Using Native Chemical Ligation: The Functional Role of Ser17 Phosphorylation in MDM2 Reexamined
inferredcites →https://doi.org/10.1021/ja800201jopenalex-snapshot
Quantitative Lid Dynamics of MDM2 Reveals Differential Ligand Binding Modes of the p53-Binding Cleft
inferredcites →https://doi.org/10.1021/ja804289gopenalex-snapshot
Multiple Peptide Conformations Give Rise to Similar Binding Affinities: Molecular Simulations of p53-MDM2
inferredcites →https://doi.org/10.1021/jm501092zopenalex-snapshot
Small-Molecule Inhibitors of the MDM2–p53 Protein–Protein Interaction (MDM2 Inhibitors) in Clinical Trials for Cancer Treatment
inferredcites →https://doi.org/10.1021/jp301720wopenalex-snapshot
From Coarse-Grained to Atomic-Level Characterization of Protein Dynamics: Transition State for the Folding of B Domain of Protein A
inferredcites →https://doi.org/10.1038/onc.2016.88openalex-snapshot
MDM2 oligomers: antagonizers of the guardian of the genome
inferredcites →https://doi.org/10.1038/srep31631openalex-snapshot
Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking
inferredcites →https://doi.org/10.1073/pnas.0334477100openalex-snapshot
Flexible lid to the p53-binding domain of human Mdm2: Implications for p53 regulation
inferredcites →https://doi.org/10.1073/pnas.0702265104openalex-snapshot
Characterization of protein-folding pathways by reduced-space modeling
inferredcites →https://doi.org/10.1080/07391102.2015.1031178openalex-snapshot
Computational analysis of spiro-oxindole inhibitors of the MDM2-p53 interaction: insights and selection of novel inhibitors
inferredcites →https://doi.org/10.1093/bioinformatics/btr484openalex-snapshot
COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes
inferredcites →https://doi.org/10.1093/bioinformatics/btu184openalex-snapshot
CABS-flex predictions of protein flexibility compared with NMR ensembles
inferredcites →https://doi.org/10.1093/nar/gkr431openalex-snapshot
Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions
inferredcites →https://doi.org/10.1093/nar/gkt332openalex-snapshot
CABS-flex: server for fast simulation of protein structure fluctuations
inferredcites →https://doi.org/10.1093/nar/gkt462openalex-snapshot
CABS-fold: server for the de novo and consensus-based prediction of protein structure
inferredcites →https://doi.org/10.1093/nar/gkv456openalex-snapshot
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
inferredcites →https://doi.org/10.1093/nar/gkv495openalex-snapshot
GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
inferredcites →https://doi.org/10.1111/cbdd.12474openalex-snapshot
Searching for Dual Inhibitors of the MDM 2‐p53 and MDMX ‐p53 Protein–Protein Interaction by a Scaffold‐Hopping Approach
inferredcites →https://doi.org/10.1126/science.274.5289.948openalex-snapshot
Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain
inferredcites →https://doi.org/10.1128/mcb.13.7.4107openalex-snapshot
Mapping of the p53 and mdm-2 Interaction Domains
inferredcites →https://doi.org/10.1146/annurev-biochem-060815-014710openalex-snapshot
The p53 Pathway: Origins, Inactivation in Cancer, and Emerging Therapeutic Approaches
inferredcites →https://doi.org/10.1146/annurev.biochem.77.062906.171838openalex-snapshot
Macromolecular Modeling with Rosetta
inferredcites →https://doi.org/10.1158/1535-7163.mct-14-1056-topenalex-snapshot
Small Molecule Inhibition of MDM2–p53 Interaction Augments Radiation Response in Human Tumors
inferredcites →https://doi.org/10.1371/journal.pone.0040897openalex-snapshot
Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics
inferredcites →https://doi.org/10.1371/journal.pone.0058769openalex-snapshot
A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking
inferredcites →https://doi.org/10.1371/journal.pone.0094769openalex-snapshot
PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta
inferredcites →https://doi.org/10.1371/journal.pone.0124423openalex-snapshot
8-Triazolylpurines: Towards Fluorescent Inhibitors of the MDM2/p53 Interaction
inferredcites →https://doi.org/10.1517/17460441.2015.1094458openalex-snapshot
Understanding the challenges of protein flexibility in drug design
inferredcites →https://doi.org/10.18388/abp.2004_3575openalex-snapshot
Protein modeling and structure prediction with a reduced representation.
inferredcites →https://doi.org/10.3109/00498254.2015.1010632openalex-snapshot
Pharmacokinetics and metabolism of AMG 232, a novel orally bioavailable inhibitor of the MDM2–p53 interaction, in rats, dogs and monkeys:in vitro–in vivocorrelation
inferredcites →https://doi.org/10.3389/fonc.2016.00007openalex-snapshot
Clinical Overview of MDM2/X-Targeted Therapies
inferredcites →https://doi.org/10.3390/molecules200610763openalex-snapshot
Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System
inferredcites →https://doi.org/10.4161/cc.10.1.14345openalex-snapshot
Chemical states of the N-terminal “lid” of MDM2 regulate p53 binding: Simulations reveal complexities of modulation
inferredcites →https://doi.org/10.4161/cc.20333openalex-snapshot
Why is F19Ap53 unable to bind MDM2? Simulations suggest crack propagation modulates binding

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Experimental and computational studies of novel amide analogues of ferulic acid as potential MDM2 inhibitors to retrieve p53 function
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Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein–Protein Interactions
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Recognition Dynamics of p53 and MDM2: Implications for Peptide Design
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The oncoprotein HBXIP promotes human breast cancer growth through down-regulating p53 via miR-18b/MDM2 and pAKT/MDM2 pathways
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Characterizing the conformational landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations
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