1. 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

2. 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

3. 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

4. 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

5. 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