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MDM2 case study: Computational protocol utilizing protein flexibility and data mining improves ligand binding mode predictions

https://doi.org/10.1101/054239
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What this work says

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

inferredcites →https://doi.org/10.1002/bab.1346openalex-snapshot
DNA topoisomerase‐directed anticancerous alkaloids: ADMET‐based screening, molecular docking, and dynamics simulation
inferredcites →https://doi.org/10.1002/jcc.20084openalex-snapshot
UCSF Chimera—A visualization system for exploratory research and analysis
inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot
Scalable molecular dynamics with NAMD
inferredcites →https://doi.org/10.1002/jcc.20634openalex-snapshot
A semiempirical free energy force field with charge‐based desolvation
inferredcites →https://doi.org/10.1002/jcc.21334openalex-snapshot
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
inferredcites →https://doi.org/10.1002/jcc.21643openalex-snapshot
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
inferredcites →https://doi.org/10.1002/jcc.23367openalex-snapshot
VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers
inferredcites →https://doi.org/10.1002/pros.10187openalex-snapshot
Experimental therapy of human prostate cancer by inhibiting MDM2 expression with novel mixed‐backbone antisense oligonucleotides: In vitro and in vivo activities and mechanisms
inferredcites →https://doi.org/10.1002/prot.20088openalex-snapshot
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
inferredcites →https://doi.org/10.1007/978-3-642-28965-1_2openalex-snapshot
Targeting the MDM2-p53 Protein-Protein Interaction for New Cancer Therapeutics
inferredcites →https://doi.org/10.1016/j.cell.2009.04.037openalex-snapshot
Blinded by the Light: The Growing Complexity of p53
inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
Flexible ligand docking to multiple receptor conformations: a practical alternative
inferredcites →https://doi.org/10.1016/s0065-3233(08)60210-7openalex-snapshot
Protein-Protein Interactions
inferredcites →https://doi.org/10.1021/ci4004656openalex-snapshot
Ligand Binding Mode Prediction by Docking: Mdm2/Mdmx Inhibitors as a Case Study
inferredcites →https://doi.org/10.1021/cr040426mopenalex-snapshot
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
inferredcites →https://doi.org/10.1038/ncomms8653openalex-snapshot
Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
inferredcites →https://doi.org/10.1038/sj.bjc.6602164openalex-snapshot
Targeting the p53–MDM2 interaction to treat cancer
inferredcites →https://doi.org/10.1039/c4mb00239copenalex-snapshot
Validation of a computational docking methodology to identify the non-covalent binding site of ligands to DNA
inferredcites →https://doi.org/10.1101/054239openalex-snapshot
MDM2 case study: Computational protocol utilizing protein flexibility and data mining improves ligand binding mode predictions
inferredcites →https://doi.org/10.1101/cshperspect.a000919openalex-snapshot
The Tumor Suppressor p53: From Structures to Drug Discovery
inferredcites →https://doi.org/10.1109/robot.2001.932674openalex-snapshot
Molecular docking: a problem with thousands of degrees of freedom
inferredcites →https://doi.org/10.1110/ps.062501507openalex-snapshot
Efficient molecular docking of NMR structures: Application to HIV‐1 protease
inferredcites →https://doi.org/10.1111/j.1747-0285.2011.01313.xopenalex-snapshot
Selective Flexibility of Side‐Chain Residues Improves VEGFR‐2 Docking Score using AutoDock Vina
inferredcites →https://doi.org/10.1111/j.1747-0285.2012.01428.xopenalex-snapshot
Identification of FDA‐approved Drugs that Computationally Bind to MDM2
inferredcites →https://doi.org/10.1186/1472-6807-13-s1-s11openalex-snapshot
DINC: A new AutoDock-based protocol for docking large ligands
inferredcites →https://doi.org/10.1186/1758-2946-1-15openalex-snapshot
Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock
inferredcites →https://doi.org/10.1371/journal.pone.0011955openalex-snapshot
Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina
inferredcites →https://doi.org/10.1371/journal.pone.0121424openalex-snapshot
Structure- and Ligand-Based Virtual Screening Identifies New Scaffolds for Inhibitors of the Oncoprotein MDM2
inferredcites →https://doi.org/10.1371/journal.pone.0131080openalex-snapshot
Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps
inferredcites →https://doi.org/10.1517/17460441.2010.484460openalex-snapshot
Virtual screening with AutoDock: theory and practice
inferredcites →https://doi.org/10.1517/17460441.2015.1094458openalex-snapshot
Understanding the challenges of protein flexibility in drug design
inferredcites →https://doi.org/10.1517/17460441.2015.962510openalex-snapshot
Thoughts on the current assessment of Polo-like kinase inhibitor drug discovery
inferredcites →https://doi.org/10.2174/0929867311320180002openalex-snapshot
Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field
inferredcites →https://doi.org/10.2174/138161212802651580openalex-snapshot
P53 Mdm2 Inhibitors
inferredcites →https://doi.org/10.2174/156802611794863544openalex-snapshot
Accounting for Induced-Fit Effects in Docking: What is Possible and What is Not?
inferredcites →https://doi.org/10.2174/156802611794863571openalex-snapshot
Protein Flexibility and Ligand Recognition: Challenges for Molecular Modeling
inferredcites →https://doi.org/10.2174/157340911795677602openalex-snapshot
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
inferredcites →https://doi.org/10.3390/molecules190710150openalex-snapshot
Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design
inferredcites →https://doi.org/10.7555/jbr.27.20130030openalex-snapshot
The MDM2-p53 pathway revisited
inferredcites →https://doi.org/10.7750/biodiscovery.2013.8.4openalex-snapshot
Small Molecule Inhibitors of MDM2-p53 and MDMX-p53 Interactions as New Cancer Therapeutics

What points at this work

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

inferred← citeshttps://doi.org/10.1080/07391102.2016.1277784openalex-snapshot
Dynamics of fluoroquinolones induced resistance in DNA gyrase of Mycobacterium tuberculosis
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