Introduction to Software
General Information



G25.2601, Fall 1996, Thursdays 1:203:10 pm, 513 WWH Course Agenda 1. Thursday, Sep. 5 (513 WWH)
Assignment 1 (due Sep. 19): Introduction to the WWW, Sequence and structural databases, and early molecular modeling literature.
2. Thursday, Sep. 12 (513 WWH)
Assignment 2 (due Sep. 19): Retrieval of structural information from the Protein Data Bank (PDB), and the display, manipulation, and analysis of threedimensional biomolecular sturctures with the Insight II molecular graphics package. 3. Thursday, Sep. 19 (122 Meyer)
Assignment 3 (due Sep. 26): Construction and analysis of an oligopeptide with the Insight II program. 4. Thursday, Sep. 26(122 Meyer)
Assignment 4 (due Oct. 10): Generation and analysis of Ramachandran plots for a protein database and introduction to the NDB http://ndbserver.rutgers.edu
5. Thursday, Oct. 3(313 WWH) Guest Lecturer: The Nucleic Acid Database, Prof. Helen Berman, Rutgers University, Department of Chemistry, Developer of NDB http://ndbserver.rutgers.edu Assignment 5 (due Oct. 10): Readings: Levitt & Chothia (1976), Lipkowitz (1995), and Cipra (1996) 6. Thursday, Oct. 10 (513 WWH)
Assignment 6 (due Oct. 17): Molecular mechanics force fields: approximations, variations, and the assessment of results with respect to experiment and other simulations. 7. Thursday, Oct. 17 (513 WWH)
Assignment 7 (due Oct. 24): A bit of programming: nonbonded versus bonded energy computations. Read on Monte Carlo: Abagyan and Totrov (1994) and from textbooks, such as: (a) malvin Kalos & Paula A. Whitlock (1986) : Monte Carlo Methods, John Wiley & Sons, New York, and (b) Paul Bratley, Bennet L. Fox, & Linus E. Schrage (1987): A Guide to Simulation , SpringerVerlag, New York. 8. Thursday, Oct. 24
Assignment : NONE. Term project announced. 9. Thursday, Oct. 31
Assignment: Continue work on Assignment 7 ... (programming). 10. Thursday, Nov. 7(513 WWH)
Assignment 8 TERM PROJECT (due Dec. 15): The Successes (failures?) of Molecular Modeling. 11. Thursday, Nov. 14 (513 WWH)
Assignment 9 (due Dec. 5): TBA. Experiments in Geometry Structure Optimization: Minimization of Biphenyl with Insight II/Discover. Read Schlick (1992) on optimization methods in computational chemistry and the CSEP chapter on mathematical optimization by T. Schlick and G. Parks http://csep2.phy.ornl.gov/csep.html. 12. Thursday, Nov. 21(513 WWH)
Assignment 10 (due Dec. 5): A Global Optimization Contest for a Pentapeptide! 13. Thursday, Nov. 28 HAPPY THANKSGIVING! (NO CLASS) 14. Thursday, Dec. 5(513 WWH)
Assignment (due Dec. 12): Read Scheraga (1992). 15. Thursday, Dec. 12(513 WWH) Guest Lecturer: Computational Approaches to the Multiple Minima Problem, Prof. Harold Scheraga, Cornell University. Assignment TERM PROJECT due Dec. 15. 16. Friday, Dec. 13 EXAM DAY (Class Schedual  Discussion, Lecture, Etc.  TBA)!
Monday, Dec. 15 TERM PROJECT DUE!
Updated 11/11/96 