ArticleJournal of the Royal Society, Interface2011
Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs.
Article in Journal of the Royal Society, Interface, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2025Article
- Introduction to Computational Biomedicine.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Uncertainty quantification in classical molecular dynamics.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2021Article
- Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics.Frontiers in oncology · 2021Review
- Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors.Interface focus · 2020Article
- Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction.Interface focus · 2020Review
- Application of the ESMACS Binding Free Energy Protocol to a Multi-Binding Site Lactate Dehydogenase A Ligand Dataset.Advanced theory and simulations · 2020Article
- Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4.Scientific reports · 2019Article
- High-throughput binding affinity calculations at extreme scales.BMC bioinformatics · 2018Article
- Uncertainty Quantification in Alchemical Free Energy Methods.Journal of chemical theory and computation · 2018Article
- An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2017Article
- Epidermal growth factor receptor (EGFR) mutations in small cell lung cancers: Two cases and a review of the literature.Lung cancer (Amsterdam, Netherlands) · 2016Review
- The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study.EBioMedicine · 2015Article
- Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors.Journal of chemical theory and computation · 2014Article
- Computational study of EGFR inhibition: molecular dynamics studies on the active and inactive protein conformations.Journal of molecular modeling · 2013Article
- Cell targeting with hybrid Qβ virus-like particles displaying epidermal growth factor.Chembiochem : a European journal of chemical biology · 2011Article
- Clinically driven design of multi-scale cancer models: the ContraCancrum project paradigm.Interface focus · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The epidermal growth factor receptor (EGFR) is a major target for drugs in treating lung carcinoma. Mutations in the tyrosine kinase domain of EGFR commonly arise in human cancers, which can cause drug sensitivity or resistance by influencing the relative strengths of drug and ATP-binding. In this study, we investigate the binding affinities of two tyrosine kinase inhibitors--AEE788 and Gefitinib--to EGFR using molecular dynamics simulation. The interactions between these inhibitors and the EGFR kinase domain are analysed using multiple short (ensemble) simulations and the molecular mechanics/Poisson-Boltzmann solvent area (MM/PBSA) method. Here, we show that ensemble simulations correctly rank the binding affinities for these systems: we report the successful ranking of each drug binding to a variety of EGFR sequences and of the two drugs binding to a given sequence, using petascale computing resources, within a few days.
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