Fall 2004

Instructor:  Dr. Abby Parrill

General Course Information

• Syllabus
• Semester Calendar
• Second Peer Review Form (Research Update)
• Conformational distribution sample spreadsheet
• Coupling constants from torsion angles sample spreadsheet

Class Notes 2004

• Topic 1: Introduction, Visualization and Public Structure Databases (Handout)
• Topic 2: Molecular Mechanics (Handout)
• Topic 3: Geometry Optimization (Handout, updated 9/10/04)
• Topic 4: Conformational Searching (Handout, updated 9/10/04)
• Topic 5:  Coarse-Grained Modeling (Handout, updated 10/20/04)
• Topic 6: Energetics (Handout, updated 9/21/04)
• Topic 7:  Guiding Conformational Searches with Experimental Information (Handout, updated 9/21/04)
• Topic 8:  Molecular Dynamics (Handout, updated 9/28/04)
• Topic 9: Solvation (Handout, updated 9/30/04)
• Topic 10:  Protein Modeling (Handout, updated 10/18/04)
• Topic 11:  QSAR (Handout, updated 10/18/04)
• Topic 12:  Docking (Handout, updated 10/20/04)
• Topic 13:  De novo design (Handout, updated 10/26/04)
• Topic 14:  Transition State Modeling (Handout)
• Topic 15:  Modeling Lipids and DNA (Handout)
• Topic 16:  Combined Methods - QM/MM
• Topic 17:  Clustering and Combinatorial Chemistry (Handout, updated 11/29/2004)
• Topic 18:  Forcefield Parameterization (Handout, updated 11/29/2004)
• Topic 19:  Modeling Organometallic Systems in the MM Formalism (Handout, updated 11/29/2004)
• Topic 20:  Artificial Intelligence in Chemistry (Handout, updated 11/29/2004)
• Topic 21:  Introduction to Unix (Handout, updated 11/29/2004)

Helpful Web Resources

• The Protein Databank
• GeneBank
• Cambridge Crystallographic Data Centre
• Reciprocal.net - a distributed crystallography network for researchers, students and the general public

Last modified 11/29/2004

Abby Parrill
Department of Chemistry
University of Memphis

These pages may be downloaded and linked from other pages freely for academic and educational purposes. Questions, problems, and errors should be sent to aparrill@memphis.edu.