| √∅ |
Slides |
Title |
|
When |
Reading |
Due |
| √ |
Lecture 1 |
Intro to proteins |
PDF |
Tue, Jan 26 |
|
|
|
| √ |
Lecture 2 |
Where do proteins come from? |
PDF |
Fri, Jan 29 |
PDB vid |
|
|
| √ |
Lecture 3 |
Protein Classification |
PDF |
Tue, Feb 2 |
|
|
|
| ∅ |
Lecture 4 |
Structural Homology |
PDF |
Fri, Feb 5 |
|
|
|
| ∅ |
Lecture 5 |
Barnase/Barstar interactions |
PDF |
Tue, Feb 9 |
HW 1 |
|
|
| ∅ |
Lecture 6 |
Molecular Dynamics |
PDF |
Fri, Feb 12 |
|
|
|
| ∅ |
Lecture 7 |
Normal Mode Analysis |
PDF |
Tue, Feb 16 |
|
|
|
| ∅ |
Lecture 8 |
Electrostatic surfaces |
PDF |
Fri, Feb 19 |
|
|
|
| ∅ |
Lecture 9 |
Force field |
PDF |
Tue, Feb 23 |
|
|
|
| ∅ |
Lecture 10 |
Energy Minimization |
PDF |
Fri, Feb 26 |
|
|
|
| ∅ |
Lecture 11 |
Docking and drug discovery |
PDF |
Tue, Mar 2 |
|
|
|
| ∅ |
Lecture 12 |
Virtual screening, replica exchange MD |
PDF |
Fri, Mar 5 |
|
|
|
| ∅ |
Lecture 13 |
Review |
PDF |
Tue, Mar 9 |
|
|
|
| ∅ |
Lecture 14 |
Midterm |
PDF |
Fri, Mar 12 |
|
|
|
| ∅ |
Lecture 15 |
Nilesh Banavali, strucutre function problems |
PDF |
Tue, Mar 16 |
|
|
|
| ∅ |
Lecture 16 |
Hongmin Li, structure-based drug design |
PDF |
Fri, Mar 19 |
|
|
|
| ∅ |
Lecture 17 |
Covalent drugs and fragment-based drug discovery |
PDF |
Tue, Mar 23 |
|
|
|
| ∅ |
Lecture 18 |
Protein local structure |
PDF |
Fri, Mar 26 |
|
|
|
| ∅ |
Lecture 19 |
Side chain rotamers |
PDF |
Tue, Mar 30 |
|
|
|
| ∅ |
Lecture 20 |
Homology modeling |
PDF |
Fri, Apr 2 |
tutorial |
|
|
| ∅ |
Lecture 21 |
Voids and waters |
PDF |
Tue, Apr 6 |
|
|
|
| ∅ |
Lecture 22 |
Validation of models |
PDF |
Fri, Apr 9 |
|
|
|
| ∅ |
Lecture 23 |
Phylogenetic analysis |
PDF |
Tue, Apr 13 |
|
|
|
| ∅ |
Lecture 24 |
Quaternary structure |
PDF |
Fri, Apr 16 |
|
|
|
| ∅ |
Lecture 25 |
Modeling nucleic acids |
PDF |
Tue, Apr 20 |
|
|
|
| ∅ |
Lecture 26 |
Protein design workshop |
PDF |
Fri, Apr 23 |
|
|
|
| ∅ |
Lecture 27 |
Student presentations |
PDF |
Tue, Apr 27 |
|
|
|
| ∅ |
Lecture 28 |
Review |
PDF |
Fri, Apr 30 |
|
|
|
| |
|
Final exam |
|
TBD |
|
|
|
| go to Blackboard |
