• Your Presentations!!!
• Exam II Material
• Exam I Material
  • Answer Key
  • CHIME-based answers to question 2:
    • Parts C and E
    • Parts A and B
    • Part D
• DNA Exploration or DNA Tutor (some buttons have slow animations on Macs - be patient).

  tRNA	Hammerhead	Group I Riboz	Leadzyme	G-quartet RNA
  AMP Aptamer	Arg Aptamer	HIV Peptide Aptamer	Pseudoknot

• Aptamer Review Manuscript
• ChimeShell - a quick way to make presentations:
  • Documentation
  • Demo
• Cytochrome c Oxidase
• Plastocyanin (blue copper)
• Want to do this with your favorite sequence?
  • Go to the Swiss-Prot site. This is a sequence database (as compared with the PDB structure database).
  • Search for the Swiss-Prot accession number for your sequence. Then type that into the dialog box of the First Approach Mode modeler. Alternatively, paste in your entire protein sequence.
  • Proceed as above. Let us know how it works out!
• Lecture Note Figures:
  • Protein Engineering
• Old Class assignments:
  • Assignment #1 (was due 2/12)
  • Assignment #2 (was due 2/25 before class)
  • 2/25/99   The following class assignment should have been completed by last Thursday (3/4).
    • Go to the Homology Modeling Tutorial. Work through the example that they give.
      • in other words, submit the sequence P41047 (Fas ligand) to the First Approach Mode modeler.
      • Wait for the results to be returned by EMail.
      • Inspect the results:
        • Take the EMail message with a subject like "SwissModel-Model-AAAa28910" and save it to a text file (In Eudora, "Save as..."). Call it "SwModel.pdb"
        • Open, using SwissPDBViewer, the file 11TNR.pdb from the tutorial folder (or download 1TNR from the pdb). This is the lymphokine receptor structure.
        • Open into SwissPDBViewer your new structure: "SwModel.pdb"
        • Now do the series: Magic Fit, Generate Structural Alignment, Iterative Magic Fit
        • Compare the two structures. Not bad. Where are the deviations?

Useful links in macromolecular modeling:

• SwissPDBViewer (application Mac/PC) - Tutorial, Download Mac or Download Windows
• Rasmol (application Mac/PC)
• CHIME (Netscape plug-in Mac/PC)

• Protein Database - Old, New (search for your favorite protein/nucleic acid)
  • Old vs new? The protein database, established at Brookhaven National Labs, was recently put out to competitive bid. A new consortium was awarded the contract and is now setting up a new site. At the moment, both old and new sites are up and running and fully (I believe) up to date with structures. Use whichever you prefer, or both. They each have their strengths...
• Biological Structure Database (including the Nucleic Acid Database)

• Many more links here!