2009-2010 UMBC SMART Teams

Qualification Task #4 – Model Design

Design a model that meets the design specifications in the following section. Email the script file of your completed model design to Julie ( jwolf@umbc.edu ). The deadline for submitting your final script file is Friday, October 30 th.

Submit a copy of the SMART Team Model Design Qualification Summary Sheet and checklist by email to Julie no later than Friday, October 30 th.

Your model design will be sent to Shannon (after review and resubmission, as necessary). Once this is completed, your team is officially QUALIFIED and you will be assigned a research mentor. Two copies of your model will be built. One copy will be for your team to keep and the other model will be a “thank you” gift for your mentor. We will use your abstract and the information that you have submitted about your model design to develop a model description sheet that will accompany your model.

Model Design Specifications

• PDB file: 3ee9 – Chain A only
• Alpha-carbon backbone format
• Design values (You must use these values):
• Backbone 300
• Hbonds 225
• Spacefill 275
• Wireframe 225
• Monitor Lines 225
• Disulfide bonds 225
• Identify secondary structures with color
• Add Hbonds to sheets
• Remove any “triangle” Hbonds
• Add monitor lines to create a stable physical model
• Display the sidechains involved in binding TRIM25
• Remember to have a clean backbone with your sidechains.

Suggestions

• Color . When you use color in your model design, we recommend that you make your selections carefully. Do NOT use black, because black does not print well. If you want to highlight a feature, chose a light color on a dark background OR a dark color on a light background. Always select bright or contrasting colors to highlight significant features, and do not use the bright colors on less significant features such as hydrogen bonds or monitor lines.
• We are here to help you! If you have questions, you may contact us by phone or email.
• Julie Wolf: 410-455-2146 or Email: jwolf@umbc.edu
• Shannon Colton: 414-277-2824 Email: colton@msoe.edu

SMART Team Model Design Qualification Summary Sheet and Checklist (email this with your script file)

For information on SMART Teams at UMBC, or to become a SMART team teacher or research mentor, contact Julie Wolf at 410-455-2146 or jwolf@umbc.edu