Genome 541

Spring 2021 Lecture Materials
Unit 4: Macromolecular structure and function

May 11
Lecture 1: Introduction to Protein Structure [slides]

Installing PyMol:

DOWNLOAD URL: https://pymol.org/ep
USERNAME: jun2021
PASSWORD: betabarrel

Installing PyRosetta:

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

Additional reading: [PyMol] [PyRosetta]

Homework #7: Due 11:59pm Friday May 21 [hw#7]


May 13
Lecture 2: Protein Structure Modeling 1: Forcefields [slides]

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


May 18
Lecture 3: 
Protein Structure Modeling 2: Structure Prediction and Protein Design [slides]

PyRosetta Demo #2: [ipynb][demo2.py]

Homework #8: Due 11:59pm Friday May 28 [hw#8][hw#8 files]

Further Reading: [Deep learning for protein structure prediction]


May 20
Lecture 4: 
Nucleic Acid Structure [slides]

PyRosetta Demo #3:  [ipynb][demo3.py]