Spring 2025 Lecture Materials
Unit 4: Macromolecular structure and function
May 13
Lecture 1: Introduction to Protein Structure [slides]
Installing PyMol:
DOWNLOAD URL: https://pymol.org/ep USERNAME: jun2021 PASSWORD: betabarrel
Installing PyRosetta:
See instructions at: http://www.pyrosetta.org/downloads USERNAME: teaching PASSWORD: scorefunction
Additional reading: [PyMol] [PyRosetta]
May 15
Lecture 2: Protein Structure Modeling 1: Forcefields [slides]
PyRosetta Demo #1: [demo1.ipynb]
May 20
Lecture 3: Protein Structure Modeling 2: Machine learning [slides]
Additional reading: [PLoS One 2011] [PLoS Comp. Bio 2017] [Nature 2021]
PyRosetta Demo #2: [demo2.ipynb]
May 22
Lecture 4: Nucleic Acid Structure [slides]
PyRosetta Demo #3: [demo3.ipynb]