hERG Inhibition

An inferential model for small molecule inhibition of the human Ether-à-go-go channel. http://jakeallensmith.com/projects/herg-inhibition/

Objectives

• Build an inferential model to identify molecular properties contributing to inhibition of the human Ether-à-go-go (hERG) ion channel.
• Generate an interactive visualization of the modeling process.

Dataset

• hERG assay data collected from the PubChem bioassay repository (https://pubchem.ncbi.nlm.nih.gov/bioassay/588834).
• Molecular descriptors calculated using RDKit and KNIME-CDK.

Contents

• app.R
  An R Shiny application producing an interactive visualization of the model fitting process.

• hERG_descriptors.csv
  The primary dataset.

• hERG_validation_descriptors.csv
  An independent test dataset.

• model_selection.Rmd
  Variable selection and model cross-validation.

• potency_model.Rmd
  A secondary analysis fitting a predictive model for hERG IC50.

• validation.Rmd
  Validation of the model against the test set.

• writeup.Rmd
  A final report.