Downloads

NOTE: The materials provided here are only for students registered in the course. Readings pertain to the lecture they are posted for, except for the many papers that are provided under Design Examples #1. The papers are provided for your reference and they build upon or help to explain background for the methods or design studies. Materials for the labs MUST BE read and printed out before lab. The labs can be found on the LABS Tab to the left. Lectures will be posted the day of class (so the links won't necessarily be active until then).

Lecture 1, Thursday 1/8: Protein Structure

  • Lecture Notes

    • Lecture 2, Friday 1/9: Homology Modeling and Intro to Lab

  • Lecture Notes

    • Lecture 3, Thursday 1/15: Protein Structure and Rosetta

  • Lecture Notes
  • Reading: On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations
  • Reading: Robust scaffolds for computational design and ideal structures

    • Lecture 4, Friday 1/16: Structure, Forces and Molecular Mechanics

  • Lecture Notes
  • Reading: The force field you will be using for MD simulations

    • Lecture 5, Thursday 1/22 Molecular Dynamics

  • Lecture Notes
  • Reading: The MD methods you will be using
  • Reading: Review of MD in Computational Design
  • Reading: Multi-pronged approach to design
  • Reading: Comparison of protein dynamics using different force fields and MD programs

    • Lecture 6, Friday 1/23: Rules for Design 1

  • Lecture Notes

    • Lecture 7, Thursday 1/29: Rules for Design 2

  • Lecture Notes

    • Lecture 8, Friday 1/30: Rules for Design 3

  • Lecture Notes

    • Lecture 9, Thursday 2/5: Rosetta

  • Lecture Notes

    • Lecture 10, Friday 2/6: When Mutations Matter

  • Lecture Notes

    • Lecture 11, Thursday 2/12: Design Examples 1

  • Lecture Notes
  • Reading: Design of catalytic polypeptides and proteins
  • Reading: Multistate approaches in computational protein design
  • Reading: Computational protein design promises to revolutionize protein engineering
  • Reading: Computational Protein Design: A Novel Path to Future Protein Drugs
  • Reading: Design applied to peptide-protein binding
  • Reading: Synthetic biology through biomolecular design and engineering

    • Lecture 12, Friday 2/13: Design Examples 2

  • Lecture Notes
  • Slide template for Lit Review

    • Thursday 2/19: Literature Review

  • Torrey, Jake, Elvin, Cooper, Hyerim, Maia, Navya, Noah, Morgan, Shivani, Naomi

    • Friday 2/20: Literature Review

  • Kellen, Oumsri, Christina, Sahana, Ron, Sam, Anna, Advaii, Rory, Catherine, Ethan

    • Thursday 2/26: Lecture 13 cont.

    Lecture 14, Friday 2/27: Design Examples 3

  • Lecture Notes

    • Lecture 15, Thursday 3/5: Design Examples 4

  • Lecture Notes

    • Lecture 16, Friday 3/6: Design Examples 5

  • Lecture Notes

    • Thursday 3/12: 588 Project Presentations

  • Friday 3/13: 588 Project Presentations