DiMaio Lab

Institute for Protein Design
University of Washington

Genome 541

Spring 2024 Lecture Materials
Unit 4: Macromolecular structure and function

May 6
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 8
Lecture 2: Protein Structure Modeling 1: Forcefields [slides]

PyRosetta Demo #1: [demo1.ipynb]

May 13
Lecture 3: 
Protein Structure Modeling 2: Structure Prediction and Protein Design [slides]

Additional reading: [PLoS One 2011] [PLoS Comp. Bio 2017] [Nature 2021]

PyRosetta Demo #2: [demo2.ipynb]

May 15
Lecture 4: 
Nucleic Acid Structure [slides]

PyRosetta Demo #3:  [demo3.ipynb]