Protein Modeling: 2010 NJSO Trial Event

The state results are online.

NOW WITH PICTURES! For questions and model returns, please email buildmodels@deposit.rcsb.org.

New to protein modeling? Check out a video of protein modeling demo and past results to see what it's all about. Resources are available from this site and from the CBM site.

Updates and tips are posted on at @buildmodels.

BEFORE THE COMPETITION:

TOOLS:

Build a model of amino acid residues 1-160 of chain B of the hemagglutinin structure 5hmg and bring it to IMPOUND.

Write a brief abstract that describes your model and how it illustrates hemagglutinin's structure and function.

The same prebuild model can be used at the regionals, state, and nationals.

Mini-toober Kit, Jmol, Molecule of the Month, PDB file for 5hmg, Other Resources

Please see the HINTS page and the Demonstration Video for a quick start.

AT THE COMPETITION:

TOOLS:

Bring your model and abstract to be impounded (first thing)!

Build a portion of the hemagglutinin structure 1htm using a browser similar to this (exact section TBA at regional; a section of neuraminidase structure 2hu4 will be modeled at the state and national level).

Answer questions about the structure, function, importance, and history of the modeled protein.

Materials will be made available for use during this exam.

Want to practice for the on-site build? A zinc finger is available in Jmol for practice.

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.

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.

Not sure what a PDB file is? This great video illustrates the connection between the PDB file and the 3D model. Video written by Peter Walters (UCSF) and animated by Graham Johnson. Music added by Mike Morales of Garland Publishing. Published in Alberts 4e 2002 by Garland.