Protein Modeling in 2012The RCSB PDB judged protein modeling events in NJ and San Diego County, CA. Please email any questions.
We'll continue to post about protein modeling, the RCSB PDB, and related educational news at New to protein modeling? This site offers updated quick hints and more. Be sure to also look at the event creator's site. For 2012, teams will model proteins involved in the regulation of apoptosis, using the story of the discovery and treatment of a rare genetic mutation as a guide. Prebuild kits are available for purchase ($32).
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| BEFORE THE COMPETITION: | TOOLS: |
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Build a model of the caspase protein found in PDB entry 1i3o, adding details that represent the important parts of the structure. Write a brief abstract that describes your model and how it illustrates the function of the structure. Bring both of these to IMPOUND. The same prebuild model can be used at the regionals, state, and nationals. note: not part of San Diego competition |
Mini-toober Kit or alternative materials PDB file for 1i3o Please see the HINTS and Folding your Toober for a quick start. |
| AT THE COMPETITION: | TOOLS: |
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Bring your model and abstract to be impounded (first thing)! Build selected regions of 1i3o for regionals, 3od8 for state, and 1hsa for nationals. Answer questions about the structure, function, importance, and history of the modeled protein.
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Material kits will be made available for use during this exam.
Molecule of the Month articles on caspases and MHC Jmol. Be prepared to select a specific amino acid in Jmol and mark it on your model Teams should also have a general understanding of protein function and structure, and be aware of the types of experiments (X-ray, NMR, cryo-EM) that produce the 3D coordinates in the PDB.
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The information used to build these protein models comes from the PDB. The molecular structures housed in the PDB range from small pieces of protein or DNA to complex machines, such as viruses and ribosomes. Each molecule plays a role in at least one biological process and has value in helping scientists unravel the mysteries of life. Their structures provide insight into these molecules' roles in fundamental biological processes and, in some cases, into their possible roles in disease or drug interactions.
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