| √ |
Which |
What |
|
When |
Who |
|
| √ |
Lecture 1 |
Intro to protein and amino acid structure. |
PDF |
Jan 24, 2012 |
cb |
| √ |
Lecture 2 |
Where do protein structures come from?
|
PDF |
Jan 27, 2012 |
cb |
HW 1 |
| √ |
Lecture 3 |
Protein classification. TOPS drawings.
|
PDF |
Jan 31, 2012 |
cb |
| √ |
Lecture 4 |
Rotation matrices. Least Squares. Superposition.
|
PDF |
Feb 3, 2012 |
cb |
wiki |
| √ |
Lecture 5 |
MOE workshop 1: Building small molecules
|
PDF |
Feb 7, 2012 |
cb |
HW 1 due |
| √ |
Lecture 6 |
MOE workshop 2: Secondary structure
|
PDF |
Feb 10, 2012 |
cb |
| √ |
Lecture 7 |
Comparative modeling 1: Alignment, Deletions
|
PDF |
Feb 14, 2012 |
cb |
HW 2 due |
| √ |
Lecture 8 |
Comparative modeling 2. Insertions
|
PDF |
Feb 17, 2012 |
cb |
HW 3 due |
| √ |
Lecture 9 |
Comparative modeling 3. Outgaps.
|
PDF |
Feb 21, 2012 |
cb |
| √ |
Lecture 10 |
Comparative modeling 4. Voids and waters.
|
PDF |
Feb 24, 2012 |
cb |
HW 4 due |
| √ |
Lecture 11 |
Comparative modeling 5. Evaluation.
|
PDF |
Feb 28, 2012 |
cb |
HW 5 due |
| √ |
Lecture 12 |
Comparative modeling 6. Interpetation and significance.
|
PDF |
Mar 2, 2012 |
cb |
HW 6 due |
| ∅ |
Lecture 13 |
Review.
|
|
Mar 6, 2012 |
cb |
HW 7 due |
| |
-------MIDTERM EXAM------- |
Mar 9, 2012 |
cb |
| |
-------spring break------- |
Mar 12-20, 2012 |
| √ |
Lecture 15 |
Molecular Surfaces. Poisson-Boltzman equation
|
PDF |
Mar 20, 2012 |
cb |
| √ |
Lecture 16 |
Force fields , Energy Minimization
|
PDF |
Mar 23, 2012 |
cb |
| √ |
Lecture 17 |
Ab initio protein structure prediction
|
PDF |
Mar 27, 2012 |
cb |
Reading assignment |
HW 8due |
| √ |
Lecture 18 |
Molecular Dynamics 1
|
PDF |
Mar 30, 2012 |
cb |
HW 9due |
| √ |
Lecture 19 |
MD 2 journal club
|
PDF |
Apr 3, 2012 |
cb |
HW 10due |
| √ |
Lecture 20 |
guest lecture Nilesh Banavali
|
PDF |
Apr 6, 2012 |
cb |
| √ |
Lecture 21 |
Normal mode analysis
|
PDF |
Apr 10, 2012 |
| √ |
Lecture 22 |
Docking 1
|
PDF |
Apr 13, 2012 |
cb |
| ∅ |
Lecture 23 |
no class
|
|
Apr 17, 2012 |
cb |
| ∅ |
Lecture 24 |
Docking 2
|
|
Apr 20, 2012 |
cb |
HW 12due |
| √ |
Lecture 25 |
Protein Design 1
|
PDF |
Apr 24, 2012 |
| √ |
Lecture 26 |
Journal club: Predicting protein structure using evolution
|
|
Apr 27, 2012 |
cb |
| ∅ |
Lecture 26 |
Review
|
|
May 1, 2012 |
cb |
| |
-----Student presentations----- |
May 4, 2012 |
| |
-----FINAL EXAM----- |
May 8, 2012 |
