A repository for Chodera Lab members to get up to speed on the foundational knowledge necessary for getting the most out of the lab!
Contained herein are a series of PDFs, Jupyter notebooks, and other resources that will help you get up to speed on the foundational knowledge necessary for getting the most out of the lab. This includes a series of tutorials on Python, Git, and other tools that are commonly used in the lab.
This repository will also act as a foundation-point for requisite knowledge for maximal success in the lab.
You do not have to know everything. This is a guide.
We have divided this guide up into four major sections: Cell biology, Biophysics, ML, and drug discovery. Each section will have a series of tutorials and resources that will help you get up to speed on the basics.
- Protein structure and methods to determine them
- Protein folding and dynamics
- Enzymology and kinetics
- Transport, Metabolism, and Channels
- Signaling, Genes, and Cancer
- Statistical mechanics
- Molecular dynamics 101
- Free energy calculations
- Binding models and chemical interactions
- Analysis of molecular dynamics
- Software tools for success
- Basics of ML
- Deep learning architectures
- Tools and best practices
- Applications in drug discovery
- Cheminformatics
- Protein-Ligand Interaction modeling
- Why the chemistry is hard
- Why the biology is hard
- Tools and Best practices