This is a seminar series to introduce students to the field of computational biology, particularly biomolecular modeling. Students will read from a preprint of Prof. Tamar Schlick’s book “Molecular modeling and simulation: an interdisciplinary guide”. There will be weekly presentations by the instructor and the students. There will be assigned reading for each session, including also some seminal papers in the field. The main topics are background on protein structure, dynamics, and analysis; introduction to theoretical approaches, including molecular dynamics and Monte Carlo simulations; and applications.
|
Week of |
Topic |
Reading |
Presenter |
|
1/21 |
Introduction to biomolecular modeling |
Ch 1 |
Prof. Izaguirre |
|
1/28 |
Applications of biomolecular modeling |
Ch 2; pap 5,34 |
Alice Ko |
|
2/4 |
Protein structure |
Ch 3; pap 8,13 |
Maureen H |
|
2/11 |
Protein construction and analysis |
Assignments 2,3 |
Yao Wang |
|
2/18 |
Theoretical approaches |
Ch 7; pap 24 |
Chengbang |
|
2/25 |
Guest lecture |
|
|
|
3/4 |
Homology contest |
Assignment 6; pap 35 |
|
|
3/18 |
Protein hierarchy |
Ch 4 |
Jesmin |
|
3/25 |
Molecular dynamics tutorial |
Assignment 8; Chs 8,12 |
Qun Ma |
|
4/8 |
Optimal MD parameter determination |
Ch 9 |
Alice Ko |
|
4/15 |
Monte Carlo/ Hybrid Monte Carlo |
Assignment 12; Ch 11 |
Scott Hampton |
|
4/22 |
Similarity and diversity |
Ch 12 |
Mark S |
|
4/29 |
|
|
Prof. Izaguirre |