Overview of the Event
Overview of the Event
The Protein Modeling Event is a Science Olympiad event developed by the MSOE Center for BioMolecular Modeling. To compete successfully, participants will explore the CBM Participant Resources and be able to:
- Understand basic features of protein structure
- Explore and manipulate protein structures using the online protein visualization webpages
- Create physical models using a foam covered wire called a Mini-Toober
There are three parts to the event
Part 1: Pre-Build Model
40% of Final Score
Every team must submit a pre-build model of a specific protein structure. The pre-build model is worth 40% of a team's final score for the event.
- The pre-build model will be created using a purchased "pre-build" Mini-Toober kit from www.3dmoleculardesigns.com, or with found materials of the participant's choosing such as KwikTwist tie-down ropes.
- The same pre-build model will be used at each level of the competition (invitational, regional and state). Participants will take their pre-build model home after each event.
- The pre-build model must be impounded prior to the beginning of the event (usually the morning of the event).
- The pre-build model should be submitted with a 4"x6" card with a written description of the model's colors and creative additions, addressing what, how, and why. Note that the format of this description has changed from prior years. Check the official rules for details.
Part 2: Jmol Exploration
30% of Final Score
The purpose of the Jmol exploration component of this year’s event is to allow students to demonstrate their skill in using Jmol to manipulate and explore a pdb file, for the purpose of learning something about the protein.
This portion of the competition is worth 30% of a team's final score for the event.
Students will be asked to provide written answers to two kinds of questions in this Part 2 component:
- Some questions will ask about the structure of the protein being explored. Examples of these types of questions might be:
- How many alpha helices are there in the structure?
- What is amino acid #23,…and what other amino acid sidechain does it interact with?
- Some questions will be asked about the pdb file for this protein. Links will be provided to appropriate pages displaying information for this pdb file entry on the Protein Data Bank web site. Examples of questions might include:
- At what university do the researchers who determined this structure work?
- What are the x,y,z coordinates of the alpha carbon of Arg56?
Part 3: Written Exam
30% of Final Score
Each team will complete an on-site exam during the competition. Exams may cover the protein topic being discussed, three-dimensional structure of related proteins, the PDB.org Molecule of the Month, or basic concepts of protein structure and biochemistry. The on-site written exam is worth 30% of a team's final score for the event.
- Carefully reviewing the "Participant Resources" on this website is the best way to prepare for the on-site exam.
- Participants will only have the competition time period to complete their on-site exam.
Levels of the Competition
The Protein Modeling Event is available at all levels of the Science Olympiad competition:
The same pre-build model will be used at each level of the competition, from invitational and regional to state and national. It will be created using a purchased "pre-build" Mini-Toober kit from 3D Molecular Designs, available at www.3dmoleculardesigns.com, or with found materials of the participants' choosing. At the end of each competition, participants will be allowed to pick up their pre-build model to use in future competition levels. It is expected that participants will continually improve upon and fine-tune their pre-build model as they work up through the levels of the competition.
A new protein wil be explored with Jmol at each level of the competition, from invitational and regional to state and national.
Onsite Visualization Environment
During the competition period, each team is expected to create an onsite model using a digital Onsite Visualization Environment. Event supervisors should make sure that their event location can properly run the digital onsite visualization environment at each student work station.
This environment can be accessed in three ways: online, through a locally running webpage, or through a stand-alone version of Jmol. Below is a short description along with a sample for each of these three options, which should allow event supervisors to test their event location and confirm that the onsite visualization environment will run correctly.
- Online (this is only a sample and does not represent this year's actual design environment) - This is simply a webpage that you will open on each onsite work station. The correct link to this website for each competition level (invitational, regional and state) will be included in the onsite kits and judging materials.
- Locally Running Webpage (this is only a sample and does not represent this year's actual design environment) - This is also a simple webpage, but it has been designed to run completely locally (no Internet connection is needed for it to display properly). Note that you need to copy all files onto each onsite work station, and not just the single .html file.
- Stand-alone Version of Jmol (this is only a sample and does not represent this year's actual design environment) - If the design environment does not work using the two methods listed above, you can run a simplified stand-alone version of Jmol using the Jmol.jar file. To launch Jmol and open the protein model, simply double click on the Jmol.jar file and drag the PDB file into the black display area. Then right click on this display area (which should now show an image of the protein) and select "console" from the expanded menu. Note that you need to copy all files onto each individual computer work station and not just the single Jmol.jar file.
All files for the onsite visualization environments will be provided as a .zip download link. This link will be sent to the email addresses provided to us when requesting materials, as well as on a printed piece of paper included with the onsite kits and judging materials that are shipped to event supervisors.
Additional Background Information
The Science Olympiad
Science Olympiad is a rigorous, interscholastic competition of over 30 events covering the disciplines of biology, earth science, chemistry, physics, computers and technology. For over 25 years, the Science Olympiad Mission Statement has been to improve student interest in science through competition and by emphasizing problem solving and understanding science concepts, through hands-on, minds-on constructivist learning.
The Protein Data Bank
The Protein Data Bank is an online archive that contains the three-dimensional coordinates for thousands of structures of proteins. These three-dimensional structure files (known as PDB Files)are determined using X-ray diffraction or NMR analysis. The files are created by giving each atom in a protein a specific set of X, Y, Z coordinates in 3D space. All protein structures that will be used and modeled in the Science Olympiad Protein Modeling Event are based on free PDB files from the Protein Data Bank.
The Molecule of the Month
The PDB Molecule of the Month has a monthly feature written by the molecular illustrator David Goodsell, called the Molecule of the Month. Each month's article focuses on a specific protein, describing its structure and function. All protein topics used in the Science Olympiad Protein Modeling Event are from past Molecule of the Month articles. Teams are expected to study the articles related to this year's proteins.
Protein Modeling Event Gallery
This Simple Photo Gallery highlights some successful pre-build and on-site models from last year's competition.
The Science Olympiad Protein Modeling Event is part of the MSOE Center for Biomolecular Modeling. Feel free to contact us with questions regarding the program, resource information on our Contact Us page.