Subject: Experiments using MM

From: Douglas_Stack/CAS/UNO/[email-masked]
Date: Wed, 8 Sep 1999 19:31:07 -0500

Dear CCLers,

In developing a molecular modeling course, I am looking for experiments that
will expand on molecular mechanics calculations into the biochemistry area.
Specifically, after  two labs of introduction to force fields and the components
that determine energy, minimization, etc., I'd like to have a lab that displays
how molecular mechanics is used to predict guest/host interactions of a protein
or DNA sequence.  We will be purchasing MacroMol as our primary molecular
mechanics package.  What I am looking for are articles involving a simple
example of relatively large biomolecules and their interactions with each other.
Other possible topics could involve the following:
1) display of molecular dynamics, i.e. the conformations possible to a protein
at room temp and how one particular conformation may be responsible for
biological activity
2) intercalation of a molecule into the base stacking of DNA
3) the effects of amino acid sequence on the conformation of a protein
4) docking of a ligand into an active site.

My use of molecular modeling is mainly quantum calculation on small organic
compounds, thus these topics are a bit foreign to me.  Any J. Chem. Ed. articles
would be ideal.

Thanks for your time, I be sure to summarize the responses.

Douglas E. Stack
Assistant Professor
Department of Chemistry
University of Nebraska at Omaha
Omaha, NE 68182-0109
(402) 554-3647
(402) 544-3888 (fax)
[email-masked]