Textbook Site:

• Nelson & Cox, Lehninger Principles of Biochemistry, 3rd ed, Worth Publishers, 2000

Protein Structures/Modeling/Bioinformatics:

• Protein Data Bank
• NIH Science on the Web
• Swiss-Model Automated Protein Modeling Server
• Swiss-Model Deep View PDB Viewer
• ExPaSy (Expert Protein Analysis System) Molecular Biology Server
• Molecules R Us
• Entrez (also contains easiest method for searching Medline)
• Protein Purification Exercises

Enzymes and Related Structures:

• Protease and Peptidases
• PCR reaction from Cold Spring Harbor
• Large ribosome subunit from Wayne Decatur (UMass Amherst)

Lysozyme:

• Structural Views from Carnegie Mellon site
• Worthington Manual (References to characteristics and how to assay)

Becoming a Scientist:

The Howard Medical Institute provides an interesting site entitled "Becoming a Scientist". Nine different scientists talk about the field of biomedical research. When we study nucleic acids, you may be particularly interested in reading the advice from Tom Cech, who won the Nobel Prize for his work on ribozymes, catalytic RNAs and is now director of HHMI

Programs to Help Visualize and Manipulate Macromolecular Structures:

RasMol
RasMol is easy to learn and allows extensive manipulation and exploration of known structures. Unless otherwise noted, the links listed for RasMol are the creation of Eric Martz at UMass Amherst. Rasmol is loaded onto the computers in rooms 230 and 215 and onto many of the Macs in public access areas, but you can also download it yourself from the UMass site and download additional pdb files.
Available tutorials and exercises:

• RasMol Gallery shows what RasMol can do
• Tutorial by Gale Rhodes provides a very throrough introduction to modeling
• Quiz on amino acids from Duane Sears at UCSB, can act as self-test of structure, pKa, bonding
• Protein Architecture overview from William McClure at Carnegie Mellon
• Molecular dynamics simulation of lipid bilayers from RasMol homesite

Chime
Chime is related to RasMol, but because it is a Netscape plug-in, structures can be accessed more easily on the Web. Unless otherwise noted, the links listed for Chime are the creation of Eric Martz of UMass Amherst. Chime is loaded onto the computers in rooms 230 and 215 and onto many of the Macs in the public clusters, but you can also download it onto your personal computer.

• Hemoglobin tutorial
• Sickle cell Hemoglobin from Paul Reisberg's Biochemistry course at Wellesley
• DNA structure tutorial

Miscellaneous:

• Graphics Site
• Molecule of the Month
• Chemical Dictionary

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