Genome 541

Spring 2020 Lecture Materials
Unit 1: Macromolecular structure and function

March 31
Lecture 1: Introduction to Protein Structure [slides]

Installing PyMol:

DOWNLOAD URL: https://pymol.org/ep
USERNAME: jun2020
PASSWORD: alphahelix

Installing PyRosetta:

DOWNLOAD URL: http://www.pyrosetta.org/dow
USERNAME: teaching
PASSWORD: scorefunction

Additional reading: [PyMol] [PyRosetta]

Homework #1: Due 11:59pm Friday April 10 Sunday April 12 [hw#1]


April 1
Lecture 2: Protein Structure Modeling 1: Forcefields [slides]

PyRosetta Demo #1: [ipynb][demo1.py]


April 7
Lecture 3: 
Protein Structure Modeling 2: Structure Prediction and Protein Design [slides]

PyRosetta Demo #2: [ipynb][demo2.py]

Homework #2: Due 11:59pm Friday April 17 [hw#2]


April 9
Lecture 4: 
Nucleic Acid Structure [slides]

PyRosetta Demo #1: [ipynb][demo3.py]

Further Reading: [Deep learning for protein structure prediction]