| Aug. 28 |
Introduction Molecular Biology |
1, [ppt] |
Student Info [pdf] |
| Aug. 30 |
Biological Databases |
4, [ppt] |
Hw1 Out [pdf] |
| Sep. 4 |
Analyzing Sequences (Alignment) |
5,
[pdf],
[ppt] |
|
| Sep. 6 |
More on Pairwise Alignment |
5,
[pdf],
[ppt] |
|
|
|
Comparing Sequences and Structures
|
| Sep. 11 |
Multiple Sequence Alignment |
5, [pdf] |
|
| Sep. 13 |
More on Multiple Sequence Alignment |
5, [pdf] |
|
| Sep. 18 |
Visualizing and Analyzing Protein Architecture |
1, m1 , [pdf] |
Hw1 Due; Hw2 Out [pdf] |
| Sep. 20 |
Classification, Annotation: Markov Chains and Markov Models |
1, m1 , [pdf] |
|
| Sep. 25 |
Hidden Markov Models |
5, [pdf] |
Rabiner Tutorial |
| Sep. 27 |
Applications of Hidden Markov Models |
5, [pdf] |
Secondary Structure Prediction |
|
|
Protein Folding and Structure Prediction
|
| Oct. 2 |
Biomolecular Simulations: Molecular Dynamics |
m2 , [pdf] |
Simulation and Proteins |
| Oc. 4 |
More on Metropolis Monte Carlo |
m2 , [pdf] |
Survey article |
| Oct. 11 |
Structure Prediction and CASP |
6, m3 , [pdf] |
|
| Oct. 16 |
Comparative Modeling |
6, m4 , [pdf] |
Hw2 Due, Hw3 Out [pdf] script |
| Oct. 18 |
Threading |
6, m4 , [pdf] |
|
| Oct. 23 |
More on threading |
6, m5 , [pdf] |
|
| Oct. 25 |
Ab-initio Methods |
6, m5 , [pdf] |
|
| Oct. 30 |
More on Ab-initio Methods |
6, m5 , [pdf] |
|
| Nov. 01 |
Fragment-based Assembly |
6, m5 , [pdf] |
|
|
|
Characterizing Protein Associations
|
| Nov. 06 |
Docking Rigid Structures |
6, m6, m7, [pdf] |
[papers] |
| Nov. 08 |
More on Rigid-body Docking |
6, m6, m7, [pdf] |
Molecular Surface
|
| Nov. 13 | Docking Flexible Structures | m6,
m7, [pdf]
| Hw3 Due, Hw4 Out[pdf] |
| Nov. 15 | More on Docking Flexible Structures | m6,
m7, [pdf]
| |
|
|
Systems Biology |
| Nov. 20 |
Overview of Systems Biology |
7, 1 ,
2 ,
[pdf] |
Reading and Presenting |
| Nov. 27 |
More on Systems Biology |
7, 1 ,
2 ,
[pdf] |
Interim Topic Report |
| Nov. 29 |
Analysis of High-throughput Data |
7, 3 ,
4 ,
[pdf] |
PCA In R |
| Dec. 4 |
Support Vector Machines |
7, 3 ,
4 ,
[pdf] |
|
Dec. 06 |
No class today |
|
|
Dec. 11 |
Project Presentations |
|
Presentations |
Dec. 13 |
Final Exam Scheduled |
|
Hw4 Due |
