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Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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CHARMM‐GUI: A web‐based graphical user interface for CHARMM
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
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CHARMM: The biomolecular simulation program
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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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Improved protein–ligand docking using GOLD
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BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures
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Free energy simulations: The meaning of the individual contributions from a component analysis
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Small Molecule Inhibitors of Protein–Protein Interactions
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Managing protein flexibility in docking and its applications
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Structure of Free MDM2 N-terminal Domain Reveals Conformational Adjustments that Accompany p53-binding
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Using Free Energy of Binding Calculations To Improve the Accuracy of Virtual Screening Predictions
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Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
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Mdm2 promotes the rapid degradation of p53
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Docking and scoring in virtual screening for drug discovery: methods and applications
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Generalized solvent boundary potential for computer simulations
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Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
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Constant pressure molecular dynamics simulation: The Langevin piston method
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The p53 inhibitors MDM2/MDMX complex is required for control of p53 activity in vivo
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Canonical dynamics: Equilibrium phase-space distributions
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In Vivo Activation of the p53 Pathway by Small-Molecule Antagonists of MDM2
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Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain
inferredcites →https://doi.org/10.1146/annurev.biochem.77.060806.091238openalex-snapshot
Structural Biology of the Tumor Suppressor p53
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DOCK 6: Combining techniques to model RNA–small molecule complexes
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Optimal Clustering for Detecting Near-Native Conformations in Protein Docking
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Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme
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Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials
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Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain
inferredcites →https://doi.org/10.4161/cc.8.8.8185openalex-snapshot
High affinity interaction of the p53 peptide-analogue with human Mdm2 and Mdmx
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Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery
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Differential binding of p53 and nutlin to MDM2 and MDMX: Computational studies
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