Mathmol Library
http://www.nyu.edu/pages/mathmol/library/
A library of molecular models for biochemistry, in many formats.
Biochemistry
http://www.bio.cmu.edu/courses/03231/LecF04/LecLinks.html
A general biochemistry course, with links to molecular structures.
ExPASy Molecular Biology Server
http://swissmodel.expasy.org/course/text/chapter4.htm
An illustrated outline of protein structures at various levels.
Proteomics
http://ca.expasy.org/tools/
Links to ways to perform proteomic analyses.