BIOEN 488/588 :: Downloads

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 at least the day before class (so the links won't necessarily be active until then).

Lecture 1, Thursday 1/4: Protein Structure

Lecture Notes

Lecture 2, Friday 1/5: Homology Modeling and Intro to Lab

Lecture Notes

Lab 1, Fri 1/5: Intro to Sequence, Structure, and Homology Modeling with MODELLER

Go to Labs Tab (left) to read and download the labs before class.

Reading: Keizer et al., Structure of a Pilin Monomer from Pseudomonas aerguinosa: Implications for the Assembly of Pili

Reading: Campbell et al., Interaction of a Bacterially Expressed Peptide from the Receptor Binding Domain of Pseudomonas aeruginosa Pili Strain PAK with a Cross-Reactive Antibody: Conformation of the Bound Peptide

Reading: Campbell et al., Interaction of the Receptor Binding Domains of Pseudomonas aeruginosa Pili Strains PAK, PAO, KB7, and P1 to a Cross-reactive Antibody and Receptor Analog: Implications for Synthetic Vaccine Design

Reading: Xiang, Advances in Homology Protein Structure Modeling. Not required but provided in case you want more information.

Lecture 3, Thursday 1/11: Protein Structure and Rosetta

Lecture Notes

Reading: Kabsch and Sander. On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations

Reading: Schwede, Protein Modeling: What Happened to the "Protein Structure Gap"?

Reading: Baker et al., Robust scaffolds for computational design

Lecture 4, Friday 1/12: Structure, Forces and Molecular Mechanics

Lecture Notes

Reading: Levitt et al., The force field you will be using

Lecture 5, Thursday 1/18: Molecular Dynamics

Lecture Notes

Reading: Beck and Daggett, The MD methods you will be using

Reading: Childers and Daggett, Review of MD in Computational Design

Reading: Khersonsky and Fleishman, Multi-pronged approach to design

Reading: Childers and Daggett, Comparison of protein dynamics using different force fields and MD programs

Lecture 6, Friday 1/19: MD and MD Analysis

Lecture Notes

Reading: Pace and Scholtz, A Helix Propensity Scale Based on Experimental Studies of Peptides and Proteins

Reading: Fuchs and Alix, High Accuracy Prediction of β-Turns and Their Types Using Propensities and Multiple Alignments

Reading: Smith et al., A Thermodynamic Scale for the β-Sheet Forming Tendencies of the Amino Acids

Reading: Smith and Regan, Guidelines for protein design: the energetics of β sheet side chain interactions

Reading: Beck et al., The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins

Lecture 7, Thursday 1/25: Rules for Design 1

Lecture Notes

Lecture 8, Friday 1/26: Rules for Design 2

Lecture Notes

Lecture 9, Thursday 2/1: Rules for Design 3

Lecture Notes

Analysis Open, Friday 2/2

Lecture 10, Thursday 2/8: Design Examples 1

Lecture Notes

Reading: Gutte and Klauser, Design of catalytic polypeptides and proteins

Reading: Davey and Chica, Multistate approaches in computational protein design

Reading: Alvizo et al., Computational protein design promises to revolutionize protein engineering