click above image for an interactive version of lysozyme

Programs to Help Visualize and Manipulate Macromolecular Structures:

   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     
              

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   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
  

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    Mage is another visualization program created by Jane and David Richardson at Duke, where the homesite is maintained. Images created in Mage are called Kinemages. Kinemages are available as companions to several texts, including yours. You can download Mage onto your personal computer.

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   Quanta (tutorial from Tom Shattuck at Colby) is a sophisticated program for modeling and is best accessed from the Silicon Graphics computers in room 215. Includes very extensive tutorials.

   Spartan (tutorial from Donald Cotter at Mt. Holyoke) is another sophisticated program for modeling. Best accessed from the Silicon Graphics computers in room 215 and includes very extensive tutorials.

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Chimera is a new package from UCSF that allows manipulation and analysis of molecular architecture.

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Protein Structures:

• Protein Data Bank
• Molecules R Us
• Entrez (also contains easiest method of searching Medline)
• Protein Purification Exercises
  

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Enzymes:

• Protease and peptidases from Lawrence Livermore Labs
  PCR reaction from Cold Spring Harbor
  
  

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Lysozyme:

• Structural Views from Carnegie Mellon site
• Worthington manual (references to characteristics and how to assay)
• Titration of lysozyme showing electrostatic potential

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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 currently Director of HHMI..

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