Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease

This repository contains data and input files for the manuscript entitled "Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease" by Heller et al. https://doi.org/10.1101/729392

Particular files include:

1. Data in comma-separated values file (.csv) or text (.txt) format
2. Jupyter Notebook files (.ipynb) showing basic plots of data
3. Mathematica notebooks (.nb) with code for kinetic modelling of ThT aggregation data
4. PLUMED input files to reproduce metadynamic metainference simulations
5. Analysis of metadynamic metainference simulations, including: a. Scripts to perform solvent-accessible surface area calculations b. Scripts to perform hydrogen bonding calculations c. Scripts to perform GROMOS clustering (contributed by maxbonomi) d. A Jupyter Notebook file detailing other analyses performed