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Protein Modeling Event - Student Resources

Onsite Exam Preparation

The Protein Modeling onsite exam is an opportunity to show how well you can connect protein structure, amino-acid chemistry, molecular interactions, and biological function.

The written exam is approximately 60% of the total event score. About half of the written-exam score will come from molecular visualization in JUDE (the Jmol User Design Environment). During the exam, your team will load and explore a protein structure and use what you observe to answer questions.

You do not need to memorize every detail in every resource on this page. Start with the 3D Molecular Designs modules, then use the additional resources only for the topics and tournament level that apply to you.

Start With These Four Steps

1. Learn the protein fundamentals

Complete Module 1: Protein Structure and This Year’s Theme before using outside resources.

You should be able to:

• Describe primary, secondary, tertiary, and quaternary protein structure.
• Recognize α-helices, β-sheets, turns, and loops.
• Explain how amino-acid side-chain properties affect protein folding and interactions.
• Explain, in general terms, how hydrogen bonds, hydrophobic interactions, ionic interactions, van der Waals interactions, and covalent interactions can stabilize protein structure.
• Describe the role of hemagglutinin in influenza infection and its binding to sialic acid receptors.

Go to Module 1: Protein Structure and This Year’s Theme

2. Practice using JUDE

Complete Module 2: Jmol Training. Molecular visualization is a major part of the onsite exam at every tournament level.

You should be able to:

• Open and orient a protein structure.
• Change colors and display formats.
• Select chains, residues, side chains, and ligands.
• Locate α-helices, β-sheets, turns, loops, and specified amino acids.
• Use molecular views to identify simple interaction regions and describe the chemical environment around a residue or ligand.

Go to Module 2: Jmol Training

3. Understand this year’s prebuild and theme protein

Complete Module 3: Designing the Prebuild Model.

The 2026–2027 prebuild represents residues 153–252 of chain A of influenza hemagglutinin from PDB 3UBE. This region includes the sialic-acid-binding site. Module 3 helps you connect the shape and side chains of this region to receptor binding, influenza infection, and the functionally relevant features you may add to your model.

Go to Module 3: Designing the Prebuild Model

4. Use the rules to set your scope for each tournament

The expected depth increases at each tournament level. Focus first on material that applies to your next tournament.

• Regional and Invitational: Build a strong foundation in protein structure, amino-acid chemistry, influenza/hemagglutinin basics, and JUDE navigation.
• State: Apply those foundations to binding sites, mutations, simple enzyme models, allostery, post-translational modifications, and more detailed JUDE analysis.
• National: Integrate multiple concepts to analyze structures, variants, interfaces, folding, and simple structural-method information.

Read the official Protein Modeling rules

What To Study By Level

Regional and Invitational

At Regional and Invitational tournaments, focus on foundational protein biology and straightforward molecular visualization.

You should be able to:

• Identify the four levels of protein structure and relate them to protein shape.
• Recognize α-helices, β-sheets, turns, and loops.
• Classify amino-acid side chains as hydrophobic, polar, acidic, basic, aromatic, or otherwise distinctive, such as cysteine.
• Explain how side-chain properties influence whether residues tend to be buried or exposed in a folded protein.
• Identify common interactions that help stabilize proteins: hydrogen bonds, hydrophobic interactions, van der Waals interactions, ionic interactions, and disulfide bonds.
• Describe, qualitatively, why the peptide bond restricts rotation in the protein backbone.
• Explain how pH, temperature, or ionic strength can change protein structure or function in simple examples.
• Describe the general role of hemagglutinin in binding sialic acid receptors during influenza infection.
• Use JUDE to find residues, secondary structures, ligands, and simple interaction regions.

At this level, you should not be expected to recall functions of specific residues discussed only in the annual theme paper.

State Tournament

At State, build on the Regional foundation by applying protein concepts in more detail.

You may be asked to:

• Explain how multiple interactions and side-chain properties contribute to local packing, stability, or binding.
• Apply protein structure–function ideas to active sites, binding sites, or simple regulatory mechanisms.
• Compare lock-and-key and induced-fit models and interpret basic allostery examples, such as hemoglobin.
• Explain qualitatively how phosphorylation, palmitoylation, or glycosylation can affect a protein’s location, stability, or interactions.
• Use examples to explain how amino-acid substitutions in hemagglutinin may affect receptor binding, host range, or immune recognition.
• Use JUDE to identify several residues in a binding site or interface and explain how their chemical properties support ligand binding.

You will not be expected to perform enzyme-kinetics, Henderson–Hasselbalch, pKa, isoelectric-point, or similar biochemical calculations.

National Tournament

At Nationals, be prepared to integrate structure, chemistry, visualization, and annual-theme context.

You may be asked to:

• Explain how several kinds of interactions contribute to protein folding, domain stability, or protein interfaces.
• Interpret qualitative examples involving protein folding landscapes or how mutations can affect stability and conformation.
• Apply structure–function reasoning to multi-residue binding sites, conformational changes, and cooperative or allosteric effects.
• Explain how environmental changes, post-translational modifications, or mutations could affect protein activity when an example is provided.
• Analyze hemagglutinin receptor specificity, infection mechanisms, immune recognition, escape, or evolution using annual-theme materials.
• Compare related structures or variants in JUDE.
• Recognize simple structural-method information, such as a resolution value or whether a type of map/data is associated with X-ray crystallography, cryo-EM, or NMR.

Practice Molecular Visualization

Your Event Supervisor may provide 3UBE or another protein structure that is related to the annual theme. Use JUDE practice to become comfortable exploring an unfamiliar structure, not just the prebuild file.

Regional and Invitational JUDE practice

Practice these tasks until you can do them quickly:

• Find a specified chain or residue.
• Display a selected residue as sticks or space-filling atoms.
• Find and identify an α-helix, β-sheet, turn, or loop.
• Locate a ligand.
• Identify a likely hydrogen-bonding, ionic, or hydrophobic contact region from a guided molecular view.

State JUDE practice

In addition to Regional skills, practice:

• Finding several residues near a ligand or protein–protein interface.
• Comparing the properties of residues in a binding site.
• Explaining how a local chemical environment could support sialic-acid binding.
• Comparing interaction patterns between structures or variants when guided by the question.

National JUDE practice

In addition to State skills, practice:

• Comparing related protein structures or variants.
• Connecting a structural difference to a possible functional difference.
• Using a provided figure, table, or short passage from the theme paper alongside a JUDE visualization.

Quick Reference: Where to Start

Additional Study Resources

The resources below are optional references. They may contain material beyond the event scope. Use the listed resource for the named topic—do not assume you need to study an entire textbook, playlist, or course.

Amino Acids and Protein Structure

LibreTexts: Amino Acids and Side-Chain Properties
Use this resource to review hydrophobic, polar, charged, aromatic, and other side-chain properties and how they influence protein structure.

• Regional: Read selected sections on side-chain categories and qualitative structure–function effects.
• State and National: Use as a deeper reference when you need more detail about amino-acid chemistry.

Open LibreTexts: Amino Acids and Side-Chain Properties

AK Lectures: Introduction to Proteins
These videos provide visual explanations of amino acids, protein structure, and noncovalent interactions.

• Regional: Optional selected videos for teams wanting extra explanation.
• State and National: Recommended for deeper review of side-chain chemistry and protein interactions.

Open AK Lectures: Introduction to Proteins

Peptide Bonds and Protein Folding

EMBL–EBI: The Peptide Bond and Primary Structure
Use this resource to understand how peptide bonds connect amino acids and why the backbone has limited rotational freedom.

• Regional: Use only if you want an extra explanation of the qualitative peptide-bond concepts in the rules.
• State and National: Recommended for qualitative understanding of backbone constraints and protein conformation.

Open EMBL–EBI: The Peptide Bond and Primary Structure

EMBL–EBI: The Protein Folding Problem
This resource introduces protein folding, Anfinsen’s work, and Levinthal’s paradox.

• State: Optional enrichment.
• National: Recommended background for questions about qualitative folding concepts and folding landscapes.

Open EMBL–EBI: The Protein Folding Problem

Structural Biology Methods

RCSB PDB-101: Methods for Determining Structure
Use this resource to learn the basic purposes of X-ray crystallography, cryo-electron microscopy, and NMR spectroscopy.

• Regional: Not required.
• State: Optional background only.
• National: Recommended for simple questions about method recognition, map/data types, and resolution.

Open RCSB PDB-101: Methods for Determining Structure

Topics You Do Not Need To Study

The event does not require:

• Henderson–Hasselbalch calculations.
• pKa, net-charge, buffering, or isoelectric-point calculations.
• Michaelis–Menten equations, calculations, or derivations.
• Detailed Ramachandran-plot interpretation.
• Detailed electron-density or cryo-EM map fitting.
• Memorization of specific theme-paper residues at Regional or Invitational tournaments.

Focus your time on understanding how protein structure supports protein function and on using JUDE to support your answers.

Suggested Study Plan

New teams or Regional teams

• Complete Modules 1–3.
• Practice JUDE in Module 2 at least twice.
• Review amino-acid side-chain categories.
• Practice explaining how a side chain or interaction supports protein stability or binding.
• Review the general influenza infection cycle and hemagglutinin’s role.

State teams

• Complete all Regional preparation.
• Revisit Module 3 and the annual theme paper.
• Practice more detailed JUDE binding-site questions.
• Review qualitative enzyme models, allostery, and the three named post-translational modifications.
• Practice explaining possible effects of mutations or environmental changes.

National teams

• Complete all State preparation.
• Use the folding and structural-method resources listed above.
• Practice comparing related structures or variants in JUDE.
• Read annual-theme materials closely and practice using evidence from a figure, table, or molecular view to support a conclusion.
• Prioritize explanation and interpretation over memorization.

A Final Reminder

Strong Protein Modeling teams do not just identify structures—they explain what those structures mean. When preparing for the onsite exam, practice answering questions in this pattern:

• What do I observe in the structure?
• What chemical properties or interactions are involved?
• How could those features support the protein’s function?

That structure–function reasoning is useful at every tournament level.

Additional Links and Resources

• Prebuild Kits: Protein Structure Modeling Kit
• Division C Official Rules: 2027 Rules | Science Olympiad
• Science Olympiad Protein Modeling Resources: Protein Modeling | Science Olympiad