3 hours credit
Ten students maximum

This course will be aWebCt based  introduction to the use of computer
software for the analysis molecular structure.This course will focus on the
use of computer software for the visualization of macromolecular structure
and function. Consequently the course format will be a combination of lecture
and lab with emphasis being with hands-on software use.
Participants will make use of the BioMolecular Computing Resource's
SYBYL molecular modeling software. Other molecular viewing software
will be introduced including Alchemy, AMBER, MacroModel, MODELLER,
MOPAC2000, HYPERCHEM, RASMOL ,SwissPDBViewer,Look and a
postscript drawing program called MOLSCRIPT. Three public Silicon
Graphics workstations in the library and any PC or MAC on the campus
ethernet which have X-server software can access and use the SYBYL software.
Course topics will include but not be limited to the following:

 -Location and retrieval of 3D structures of macromolecules.
 -Visualization of 3D structure; production of graphic output.
 -Ligand Binding/Docking
 -Structural Principles:Molecular Energy; molecular mechanics and
           dynamics
 -Structure Modification; Site directed mutagenesis; protein
           engineering
 -Structure from data; Distance Geometry(DGEOM)
 -Structure from Net  sources
 -Structure Prediction; Homology modeling, neural net methods

 Students will be required to present both written and oral
summaries of a modeling project of personal interest at the end of
the semester. Grades will be based on the completion of various
learning tutorials and upon the project. Class time will be devoted
to various combinations of background theory, paper review, and
hands-on experience. The course will require two- to five hours
per week of non-classroom time. There will be numerous bundles
of hand-out material but no formal textbook. Those of you who
wish to audit the course are, of course welcome, BUT I hope that
you will agree to participate in class discussions and provide an
overview of your research interest in molecular modeling at some
point during the semester.