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

[1]  Mateusz Kurcinski,et al.  Highly Flexible Protein-Peptide Docking Using CABS-Dock. , 2016, Methods in molecular biology.

[2]  A. Kolinski,et al.  Coarse-Grained Protein Models and Their Applications. , 2016, Chemical reviews.

[3]  A. Fersht,et al.  The p53 Pathway: Origins, Inactivation in Cancer, and Emerging Therapeutic Approaches. , 2016, Annual review of biochemistry.

[4]  Vincent A. Voelz,et al.  Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking , 2016, Scientific Reports.

[5]  Yang Zhang,et al.  MDM2 oligomers: antagonizers of the guardian of the genome , 2016, Oncogene.

[6]  Lulu Cai,et al.  Computational analysis of spiro-oxindole inhibitors of the MDM2-p53 interaction: insights and selection of novel inhibitors , 2016, Journal of biomolecular structure & dynamics.

[7]  David M. Thomas,et al.  Clinical Overview of MDM2/X-Targeted Therapies , 2016, Front. Oncol..

[8]  D. Lane,et al.  Recognition Dynamics of p53 and MDM2: Implications for Peptide Design. , 2016, The journal of physical chemistry. B.

[9]  Mateusz Kurcinski,et al.  Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking. , 2015, Methods.

[10]  L. Kavraki,et al.  Understanding the challenges of protein flexibility in drug design , 2015, Expert opinion on drug discovery.

[11]  Vincent A. Voelz,et al.  Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics , 2015, Proteins.

[12]  Martin Zacharias,et al.  Fully Blind Peptide-Protein Docking with pepATTRACT. , 2015, Structure.

[13]  J. Lunec,et al.  Searching for Dual Inhibitors of the MDM2‐p53 and MDMX‐p53 Protein–Protein Interaction by a Scaffold‐Hopping Approach , 2015, Chemical biology & drug design.

[14]  Min Jiang,et al.  Pharmacokinetics and metabolism of AMG 232, a novel orally bioavailable inhibitor of the MDM2–p53 interaction, in rats, dogs and monkeys: in vitro–in vivo correlation , 2015, Xenobiotica; the fate of foreign compounds in biological systems.

[15]  P. Harari,et al.  Small Molecule Inhibition of MDM2–p53 Interaction Augments Radiation Response in Human Tumors , 2015, Molecular Cancer Therapeutics.

[16]  Mateusz Kurcinski,et al.  Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System , 2015, Molecules.

[17]  Hasup Lee,et al.  GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization , 2015, Nucleic Acids Res..

[18]  J. Andréasson,et al.  8-Triazolylpurines: Towards Fluorescent Inhibitors of the MDM2/p53 Interaction , 2015, PloS one.

[19]  Mateusz Kurcinski,et al.  CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site , 2015, Nucleic Acids Res..

[20]  D. Bernard,et al.  Small-Molecule Inhibitors of the MDM2–p53 Protein–Protein Interaction (MDM2 Inhibitors) in Clinical Trials for Cancer Treatment , 2014, Journal of medicinal chemistry.

[21]  Liu Liu,et al.  Case Study: discovery of inhibitors of the MDM2-p53 protein-protein interaction. , 2015, Methods in molecular biology.

[22]  T. Hoffmann,et al.  Peptide therapeutics: current status and future directions. , 2015, Drug discovery today.

[23]  Mateusz Kurcinski,et al.  Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations. , 2014, Journal of chemical theory and computation.

[24]  Sebastian Kmiecik,et al.  Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors , 2014, Biophysical journal.

[25]  Haiou Li,et al.  PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta , 2014, PloS one.

[26]  Adelene Y. L. Sim,et al.  Mechanism of Stapled Peptide Binding to MDM2: Possible Consequences for Peptide Design. , 2014, Journal of chemical theory and computation.

[27]  Andrzej Kolinski,et al.  CABS-flex predictions of protein flexibility compared with NMR ensembles , 2014, Bioinform..

[28]  Alexander Dömling,et al.  Transient protein states in designing inhibitors of the MDM2-p53 interaction. , 2013, Structure.

[29]  Qing-Chuan Zheng,et al.  Molecular dynamics simulations studies and free energy analysis on inhibitors of MDM2-p53 interaction. , 2013, Journal of molecular graphics & modelling.

[30]  Andrzej Kolinski,et al.  CABS-fold: server for the de novo and consensus-based prediction of protein structure , 2013, Nucleic Acids Res..

[31]  Andrzej Kolinski,et al.  CABS-flex: server for fast simulation of protein structure fluctuations , 2013, Nucleic Acids Res..

[32]  Alexandre M. J. J. Bonvin,et al.  A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking , 2013, PloS one.

[33]  Gennady M Verkhivker,et al.  Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics , 2012, PloS one.

[34]  D. Lane,et al.  Why is F19Ap53 unable to bind MDM2? Simulations suggest crack propagation modulates binding , 2012, Cell cycle.

[35]  Dominik Gront,et al.  From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein A. , 2012, The journal of physical chemistry. B.

[36]  Weirong Yuan,et al.  Interrogation of MDM2 phosphorylation in p53 activation using native chemical ligation: the functional role of Ser17 phosphorylation in MDM2 reexamined. , 2012, Journal of the American Chemical Society.

[37]  Vittorio Scarano,et al.  COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes , 2011, Bioinform..

[38]  Ora Schueler-Furman,et al.  Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions , 2011, Nucleic Acids Res..

[39]  Andrzej Kolinski,et al.  Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation–Condensation to Framework Mechanism , 2011, Journal of the American Chemical Society.

[40]  Chandra S Verma,et al.  Chemical states of the N-terminal “lid” of MDM2 regulate p53 binding: Simulations reveal complexities of modulation , 2011, Cell cycle.

[41]  Nir London,et al.  Sub‐angstrom modeling of complexes between flexible peptides and globular proteins , 2010, Proteins.

[42]  Iris Antes,et al.  DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility , 2010, Proteins.

[43]  Shubhra Ghosh Dastidar,et al.  Multiple peptide conformations give rise to similar binding affinities: molecular simulations of p53-MDM2. , 2008, Journal of the American Chemical Society.

[44]  David Baker,et al.  Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.

[45]  Rafael Brüschweiler,et al.  Quantitative lid dynamics of MDM2 reveals differential ligand binding modes of the p53-binding cleft. , 2008, Journal of the American Chemical Society.

[46]  A. Kolinski,et al.  Characterization of protein-folding pathways by reduced-space modeling , 2007, Proceedings of the National Academy of Sciences.

[47]  Paul N Barlow,et al.  Structure of free MDM2 N-terminal domain reveals conformational adjustments that accompany p53-binding. , 2005, Journal of molecular biology.

[48]  H. Carlson,et al.  Computational studies and peptidomimetic design for the human p53–MDM2 complex , 2004, Proteins.

[49]  A. Kolinski Protein modeling and structure prediction with a reduced representation. , 2004, Acta biochimica Polonica.

[50]  U. Moll,et al.  The MDM2-p53 interaction. , 2003, Molecular cancer research : MCR.

[51]  M. McCoy,et al.  Flexible lid to the p53-binding domain of human Mdm2: Implications for p53 regulation , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[52]  S F Howard,et al.  Molecular characterization of the hdm2-p53 interaction. , 1997, Journal of molecular biology.

[53]  A. Levine,et al.  Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain , 1996, Science.

[54]  A. Levine,et al.  Mapping of the p53 and mdm-2 interaction domains. , 1993, Molecular and cellular biology.