Biochemistry Projects
Links to other molecular modeling applications of Jmol, Rasmol, Chime, etc. for introductory biochemistry.

Hexokinase Tutorial from which my first project really found the inspiration
Google Search for similar ideas
MolVis World Index of Molecular Visualisation Resource, International version (non-English)
Interactive Biochemistry links for tutorials
MolviZ link to tutorials primarily using a Jmol interface
Proteopedia which is basically the Wiki of proteins.
MolVis Top 5 programs for molecular viewing and tutorials.
Protein Explorer which uses First Glance and Chime.

Tutorial on Peptide and Protein Structure by J. E. Wampler.
Introduction to Protein Structure by Frank Gorga.
Interactive Protein Tutorials webpage provides a list of links to a variety of tutorials.

Scripting Examples

Jmol Applications presented by St. Olaf Chemistry Department. A variety of examples have been posted.
Callutheran introductory to Jmol scripting by David Marcey
Jmol Interactive scripts documented by Robert Hanson at St. Olaf offers an excellent source once you learn how to navigate the scripts and the examples linked below may offer more help
Interactive Jmol Examples by Robert Hanson at St. Olaf
Sourceforge basic scripting commands.
Articles of Interest from J Chem Ed.
Rough Guide to HTML constructed by members of the Chemistry Department at the University of Bristol in the UK as well as the subsequent documentation of Jmol scripts
Jmol Applet Documentation by members of the Chemistry Department at the University of Bristol

Jmol Applet uses, although primarily aimed at crystallography, constructed by faculty at University of Pennsylvania
Dr Krause's page for pattern identification in biological squences