Download Computational Structural Biology and Molecular Biophysics

Hands-on Course in
Computational Structural Biology
and Molecular Simulation
BIOP 586C / Chem 470
Emad Tajkhorshid & Zan Luthey-Schulten
Center for Computational Biology and Biophysics
Departments of Chemistry and Biochemistry
Beckman Institute
Course Details
•  Lectures: 1105 Siebel Center, Mon/Wed/Fri 1-2 pm
•  Computer Labs: Burrill Hall 164D/E, Wed/Fri. 1-3:30 pm
•  Office hours:
–  Wed/Fri 4-5pm 3009/3011/3021 Beckman
•  Lab experts:
–  Mark Arcario, Ke Chen, Tao Jiang, Jonathan Lai, Jing Li
•  Grading
–  Attendance (distributed over the hours of labs and lectures)
–  Homework/assignments
–  Term Project
Course Materials
•  Lectures in PDF:
–  Will be deposited in a web site:
csbmb.beckman.illinois.edu/BIOP586C/
•  Tutorials and files needed:
–  Will be installed on the lab machines; will be linked
also from the course web page
•  Install VMD and NAMD on your own laptop/
desktop for your term projects: MAC, PC,
Linux:
www.ks.uiuc.edu
Overview of the Course
•  Introduction to Structural Biology
•  Visualization and basic structural analysis of biological
macromolecules
•  Setup and basic analysis of molecular simulation
methods
•  Advanced simulations and analysis, steered MD,
targeted MD, …
•  Quantum mechanical treatments of molecular systems
•  Parameters and topology information
•  Bioinformatic analysis of molecular systems
•  Systems Biology
•  Simulating membrane channels and artificial model
channels
Some practical information for
Friday
•  Burrill Hall Lab password: biop586
•  Remember your desk
•  Remember the directory you are working in
•  Familiarize yourself with basic Unix and editor
commands