Biophysics 206: Computation of Biological Molecules
Course Director: Matt Jacobson
[matt.jacobson@ucsf.edu]
Spring 2008
Topics
Quantum Mechanics
- Will
be taught emphasizing conceptual understanding and deemphasizing complex
derivations
- Emphasis
on electronic structure, including Hartree-Fock, DFT, and semi-empirical
methods
Molecular Mechanics
- Force
fields
- Explicit
and implicit solvent models
- Molecular
dynamics and Monte Carlo
- Free
energy methods
Applications to drug discovery and biological problems
Schedule
All class sessions in room S261, Genentech Hall.
|
Week
|
Monday, 1-2:30
|
Wednesday, 1-2
|
|
1
|
4/7
|
QM lecture
|
Matt
|
4/9
|
QM lecture
|
Matt
|
|
2
|
4/14
|
QM lecture
|
Matt
|
4/16
|
paper discussion
|
TBA
|
|
3
|
4/21
|
QM lecture
|
Matt
|
4/23
|
paper discussion
|
TBA
|
|
4
|
4/28
|
QM lecture
|
Matt
|
4/30
|
paper discussion
|
TBA
|
|
5
|
5/5
|
Introduction to
molecular mechanics
|
Andrew
|
5/7
|
paper discussion
|
TBA
|
|
6
|
5/12
|
Molecular dynamics
|
Jed
|
5/14
|
paper discussion
|
TBA
|
|
7
|
5/19
|
5/21
|
paper discussion
|
TBA
|
|
8
|
5/26
|
Free energies
|
Andrew
|
5/28
|
paper discussion
|
TBA
|
|
9
|
6/2
|
Possible guest
lecture
|
TBA
|
6/4
|
paper discussion
|
|
Matt = Matt Jacobson
Andrew = Andrew Pohorille
Jed = Jed Pitera
Assignments
- In-class presentation. Lead a discussion on one paper from
the literature, focusing on methods discussed in class. The paper could be one of two
types: a) an application of
computational methods discussed in class to a biological system (hopefully
one that interests you), or b) a paper describing a computational method
that has not been discussed in class.
This is meant to be an in-depth critical examination of the computational
methods being used, making reference to the material covered in the
lectures: are the methods sound,
what are some alternate approaches, why is the work significant (or
not). Please let Matt know which paper you want to review before
starting to work on this, and send me your slides or notes at least one
day in advance of your presentation so we can make sure you’re on the
right track.
- Final
exam. For pre-orals
students, propose a computational study, in a mock-qualifying exam format. This will be a 45 minute oral exam with Matt
and one other member of the computational faculty. During the first 5-10 minutes, you will
outline the proposal, and then you will spend the remaining time defending
it, drawing on your knowledge from class.
You must discuss your
proposed project with Matt by the second week of May (primarily to
ensure you don’t try to bite off too much). Obviously, you should not propose your
thesis project. You should propose
at most 2 specific aims.
- Numerical
exercise. You can choose
from the following options, whatever is going to be most useful to you:
- Quantum
mechanics problem set
- Quantum
hands-on application to hydrogen bond strengths (substituted amines)
- Design
your own exercise, including applications of molecular dynamics
Stuff from prior years
Last Year's Syllabus
Last Year's Reading List
Dr. Jacobson’s work on this class is supported in part by an
NSF CAREER award, MCB-0346399.