Science Olympiad Student Team Training Resources Prebuild Model

Delineate the Scale – Start by marking the scale on your linear model. All prebuild models for the Protein Modeling Event should represent 100 amino acids at a scale of 2cm per amino acid, for a total length of 200cm.
Add Endcaps – Add a blue endcap at the beginning of your model to represent the N-terminus and a red endcap at the end of your model to represent the C-terminus.
Map Secondary Structures – Mark the beginning and end of each alpha helix and beta sheet in the 100 amino acid long protein you are modeling. These marks will guide the folding of the secondary structures.
Annotate Key Sidechains – Mark the locations of any key sidechains you plan to display so that you can add them in the correct locations once you have folded your model.

Fold the Secondary Structures – Using the annotations you added to your linear model, fold the two types of secondary structures. Alpha helices are right handed spirals and beta sheets are zig-zag shapes.
Fold the Tertiary Structure – Using the JUDE Jmol display as your guide, fold the overall shape of your protein structure. Rotating the digital display of your structure will allow you to view it from different angles, which will help you fine tune the folded shape of your physical model.
Add Sidechains and Creative Additions – Once the overall 3-dimensional shape of your protein is folded, you can begin to add creative additions to further enhance your model.

Scoring Rubrics – Event supervisors will use a prebuild scoring rubric to award points for the accuracy of your folded prebuild model. Having correctly positioned features such as the blue and red endcap, the two types of secondary structures, and the correct overall shape will earn your model points.
Creative Additions – Going beyond a correctly folded protein backbone will be crucial for competing in higher levels of the competition. Creative additions such as showing key sidechains or modeling other molecules that interact with the protein will earn your prebuild model additional points.
The Notecard – Including a notecard that clearly describes what features you have included on your model, how you have chosen to represent those features, and why you feel they were important will earn your model points (see example below).
Model Size - Prebuild models must not exceed 50cm x 50cm x 50cm

The 2025-2026 Prebuild Protein Structure

The 2025-2026 prebuild model should represent residues 1-100 of chain A of the protein structure file 2LV8.pdb.

The same prebuild protein structure will be used at all levels of the event. Teams are encouraged to improve and refine their prebuild models as they participate in higher levels of the event, as model judging will become more rigorous.

1-2

Protein Databank Reference:https://www.rcsb.org/structure/2LV8
Structure-function Summary: https://pdb101.rcsb.org/motm/70
Scientific Article: https://pmc.ncbi.nlm.nih.gov/articles/PMC3705962/
Prebuild and Invitational Event Jmol User Design Environment (JUDE): https://learn.3dmoleculardesigns.com/prebuild-jmol-user-design-environment-science-olympiad-2026
Prebuild Modeling Kits: https://shop.3dmoleculardesigns.com/products/protein-structure-modeling-kit

At all levels of the competition, the prebuild model will be judged based on two main features:

The accuracy of the overall fold of the protein model’s backbone
The creative additions used to enhance the protein model

Creative additions can make the difference between an average prebuild model and a winner. Using modeling materials of your choice, enhance your prebuild model with features that represent key concepts and structural features related to this year's protein topic and prebuild structure.

The theme of this year's protein modeling event, designer proteins, focuses on how artificial intelligence can interpret the basic principles of protein folding to create de novo stable protein structures. For that reason, the basic principles of protein folding would be an excellent area to explore for your creative additions, including:

secondary structures
hydrophobic core
hydrophilic shell
disulfide bonds
salt bridges
levels of protein structure

Note that judges can award points for other creative additions not listed here, if they are relevant to the protein structure and accurately shown. Higher levels of the competition will award a larger portion of the prebuild model score based on creative additions.

Introduction Section: Do not start with the abstract (usually the first section in a scientific paper). Rather, skip to the introduction section, which will provide some background for the content in the paper.
Identify Vocabulary: After reading the introduction, take some time to look up any vocabulary you are not familiar with. This will help you understand the remaining sections of the paper.
Images and Image Captions: Next, explore the various figures and data diagrams throughout the paper, including the captions below each of the figures.
Conclusion Section: This section will describe the primary findings of the research that was described in more detail with the figures and captions found throughout the rest of the paper.
Abstract Section: Finally, return to the abstract section, usually found at the very beginning of the paper for a wholistic overview of the research done.