(1) MSCBIO 2030/ CMPBIO 2030 -- Introduction to
Computational Structural Biology (3 credits)
(2) MSMBPH/MOLBPH 2002 -- Molecular Biophysics 2:
Theory and Simulation (3 credits)
(3) BIOINF 2052 -- Introduction to Computational Structural Biology (3
credits)
NOTE: THESE COURSES ARE LISTED SEPARATELY, BUT
THEY ARE ALL THE SAME COURSE.
Instructors: Profs. Ivet Bahar, Carlos Camacho, Daniel M. Zuckerman* – all from the Department of
Computational Biology, School of Medicine, University of Pittsburgh.
Additional lecture by Prof. C. Langmead,
CMU.
*DM Zuckerman – course coordinator
Contact Information:
Meeting Time/Place: Tuesdays & Thursdays
8:50 - 10:05
AM*, Room 3073, Biomedical Science Tower 3, University of Pittsburgh
*Beginning on Tuesday, Jan. 23, 2007
Required Textbooks:
Computer Simulation of Liquids by Allen and Tildesley and
Molecular Modelling, by Leach (Both available at the Health
Sciences Bookstore on Forbes near McKee)
Grading: Homework (45%), Exam 1 (15%), Exam 2 (15%),
Final Exam (25%)
Click here to access course materials
|
Date |
Lecturer |
Topics |
|
SECTION 1:
STRUCTURE/ENERGY |
|
Jan 4 (Th) |
Bahar |
Introduction to Computational Structural Biology |
|
Jan 9 (Tu) |
Bahar |
Macromolecular Structures and Protein Conformations |
|
SECTION 2: PROBABILITY THEORY |
|
Jan 11 (Th) |
Zuckerman |
Probability Theory I |
|
Jan 16 (Tu) |
Zuckerman |
Probability Theory II |
|
Jan 18 (Th) |
Zuckerman |
Probability Theory III |
|
SECTION 3:
STRUCTURE/ENERGY (continued) |
|
Jan 23 (Tu) |
Zuckerman |
Overview of nucleic acid and membrane structures |
|
Jan 25 (Th) |
Bahar |
Molecular Forces and Energetics (Force Fields and Knowledge-based
potentials) |
|
Jan 30 (Tu) |
Bahar |
Quantitative modeling/generation of macromolecular structures.
(Monte Carlo simulations, Markov models) |
|
Feb 1 (Th) |
**** EXAM
1**** |
|
SECTION 4: STATISTICAL
MECHANICS/BIOPHYSICS |
|
Feb 6 (Tu) |
Zuckerman |
One-dimensional statistical mechanics |
|
Feb 8 (Th) |
Zuckerman |
One-dimensional statistical mechanics – II |
|
Feb 13 (Tu) |
Zuckerman |
Multi-dimensional statistical mechanics |
|
Feb 15 (Th) |
Zuckerman |
Thermodynamics |
|
Feb 20 (Tu) |
Zuckerman |
Dielectrics, screening, solvation, hydrophobic effect |
|
Feb 22 (Th) |
Zuckerman |
Connecting dynamics and equilibrium |
|
Feb 27 (Tu) |
Bahar |
Protein
folding |
|
Mar 1 (Th) |
Zuckerman |
Binding |
|
Mar 6, 8 (Tu, Th) |
|
[NO
CLASS – SPRING BREAK] |
|
Mar 13 (Tu) |
Zuckerman |
Chemical
and enzyme kinetics |
|
Mar 15 (Th) |
**** EXAM
2**** |
|
SECTION 5:
BIOMOLECULAR SIMULATIONS |
|
Mar 20 (Tu) |
Camacho |
Force
fields, energy minimization |
|
Mar 22 (Th) |
Camacho |
Sketch of coarse-grained models |
|
Mar 27 (Tu) |
Camacho |
Solvation, electrostatics I |
|
Mar 29 (Th) |
Camacho |
Solvation, electrostatics II |
|
Apr 3 (Tu) |
Bahar |
MD
simulations |
|
Apr 5 (Th) |
Bahar |
Analysis
of trajectories |
|
Apr 10 (Tu) |
Bahar |
Normal
mode analysis, elastic network models |
|
SECTION 6:
KEY APPLICATIONS |
|
Apr 12 (Th) |
Langmead |
CS
algorithms in structural biology |
|
Apr 17 (Tu) |
Zuckerman |
Molecular mechanics & coarse-grained models in experimental structure prediction |
|
Apr 19 (Th) |
Camacho |
Protein-ligand
& protein-protein docking |
|
Apr 24 (Tu) |
Camacho |
Homology modeling |
|
Apr 26 (Th) |
**** FINAL EXAM **** |
