Course Details
Overview
This intensive five-day online training course is designed for students, researchers, and professionals who want to develop practical skills in computational protein modelling, structural visualization, and protein structure analysis.
The course introduces participants to the fundamental concepts of structural biology and progressively guides them through computational tools for exploring, visualizing, predicting, and analysing protein structures.
Starting with an introduction to protein structure and the principles of structural biology, participants will learn how to navigate the RCSB Protein Data Bank (PDB), identify suitable protein structures, retrieve structural data, and work with different protein structure file formats.
A major focus of the course is PyMOL, a widely used molecular visualization tool. Participants will learn how to visualize protein structures, identify individual chains and structural components, examine secondary structures, highlight amino acids and ligands, measure distances, and investigate molecular interactions. The training will gradually progress from basic visualization commands to more advanced structural analysis and presentation techniques.
The course will also introduce AlphaFold, an artificial intelligence-based approach for protein structure prediction. Participants will learn about the principles behind AlphaFold, how to access predicted protein structures, interpret confidence metrics, and explore the applications and limitations of AI-based protein structure prediction.
Additional computational tools and resources, including UCSF ChimeraX and other relevant platforms, will be introduced where appropriate to provide participants with a broader understanding of modern structural biology workflows.
On the final day, participants will apply their newly acquired knowledge to an independent practical project. They will select a protein of interest, retrieve or obtain its structure, visualize and analyse it using the tools introduced during the course, and present their findings.
By the end of the training, participants will have developed a practical foundation for independently exploring and analysing protein structures using modern computational tools.
Learning Objectives
By the end of this workshop, participants will be able to:
- Understand the fundamental principles of structural biology and protein architecture
- Recognize primary, secondary, tertiary, and quaternary protein structures
- Understand the importance of protein structure in biological function and molecular interactions
- Navigate the RCSB Protein Data Bank (PDB) and identify appropriate protein structures for research purposes
- Understand PDB identifiers, structural metadata, protein chains, ligands, and experimental methods
- Download, import, and manage protein structure files in different formats
- Use PyMOL for protein visualization and structural exploration
- Identify amino acids, residues, chains, secondary structures, and ligands
- Customize molecular representations, colors, and visualization settings
- Measure distances and angles and investigate structural relationships
- Visualize binding sites and examine protein–ligand interactions
- Perform basic and advanced structural comparisons and alignments
- Understand the fundamental principles of AlphaFold and AI-based protein structure prediction
- Access and interpret AlphaFold-predicted protein structures
- Understand AlphaFold confidence metrics, including pLDDT and PAE
- Recognize the advantages and limitations of computational protein modelling
- Combine different computational tools to perform a basic protein structure analysis workflow
- Develop and present an independent protein modelling project
Target Audience
This course is particularly suitable for:
- Bachelor’s and master’s students in biology, biochemistry, biotechnology, and related disciplines
- PhD students and early-career researchers
- Researchers working in molecular biology, neuroscience, structural biology, and biomedical sciences
- Research assistants and laboratory professionals interested in computational approaches
- Scientists interested in protein structure prediction and molecular visualization
- Beginners who want to develop practical skills in computational protein analysis
- Researchers who want to expand their knowledge of AI-based protein modelling tools
No previous experience with PyMOL or computational protein modelling is required. Basic familiarity with proteins and molecular biology is helpful but not essential.
Course Program
Day 1: Introduction to Structural Biology and Protein Data Resources
Focus: Understanding protein structures and learning how to find and retrieve structural data.
| Time | Activity | Format |
|---|---|---|
| 09:00 – 09:30 | Introduction and Course Overview | Lecture |
| 09:30 – 10:30 | Fundamentals of Structural Biology and Protein Architecture | Lecture |
| 10:30 – 10:45 | Coffee Break | |
| 10:45 – 12:00 | Protein Structure: Primary, Secondary, Tertiary and Quaternary Levels | Lecture |
| 12:00 – 12:30 | Introduction to Structural Determination Methods: X-ray Crystallography, NMR and Cryo-EM | Lecture |
| 12:30 – 13:30 | Lunch Break | |
| 13:30 – 14:30 | Introduction to the RCSB Protein Data Bank (PDB) | Demonstration |
| 14:30 – 15:15 | Searching, Selecting and Downloading Appropriate Protein Structures | Practical Exercise |
| 15:15 – 15:30 | Coffee Break | |
| 15:30 – 16:30 | Understanding PDB Files, Chains, Residues, Ligands and Structural Metadata | Practical Exercise |
Day 2: Introduction to PyMOL and Basic Protein Visualization
Focus: Learning to navigate PyMOL and visualize protein structures.
| Time | Activity | Format |
|---|---|---|
| 09:00 – 09:30 | Review of Day 1 and Introduction to PyMOL | Discussion |
| 09:30 – 10:30 | PyMOL Interface, Commands and Basic Navigation | Demonstration |
| 10:30 – 10:45 | Coffee Break | |
| 10:45 – 12:00 | Loading Protein Structures and Understanding Molecular Representations | Practical Exercise |
| 12:00 – 12:30 | Visualizing Secondary Structures: Helices, Sheets and Loops | Practical Exercise |
| 12:30 – 13:30 | Lunch Break | |
| 13:30 – 14:30 | Selecting Chains, Residues, Amino Acids and Ligands | Practical Exercise |
| 14:30 – 15:15 | Colouring, Labelling and Customizing Protein Structures | Practical Exercise |
| 15:15 – 15:30 | Coffee Break | |
| 15:30 – 16:30 | Creating, Saving and Exporting High-Quality Protein Images | Guided Exercise |
Day 3: Advanced PyMOL and Structural Analysis
Focus: Exploring protein interactions, structural features, and advanced visualization techniques.
| Time | Activity | Format |
|---|---|---|
| 09:00 – 09:30 | Review of Basic PyMOL Commands | Discussion |
| 09:30 – 10:30 | Advanced Selection Commands and Molecular Representations | Demonstration |
| 10:30 – 10:45 | Coffee Break | |
| 10:45 – 12:00 | Measuring Distances, Angles and Structural Relationships | Practical Exercise |
| 12:00 – 12:30 | Identifying Binding Sites, Ligands and Important Amino Acid Residues | Practical Exercise |
| 12:30 – 13:30 | Lunch Break | |
| 13:30 – 14:30 | Investigating Protein–Ligand Interactions and Hydrogen Bonds | Practical Exercise |
| 14:30 – 15:15 | Protein Alignment and Structural Comparison | Demonstration and Exercise |
| 15:15 – 15:30 | Coffee Break | |
| 15:30 – 16:30 | Introduction to Advanced Visualization and UCSF ChimeraX | Demonstration |
Day 4: AlphaFold and AI-Based Protein Structure Prediction
Focus: Understanding modern protein structure prediction approaches and integrating predicted structures into structural analysis.
| Time | Activity | Format |
|---|---|---|
| 09:00 – 09:30 | Introduction to Computational Protein Modelling | Lecture |
| 09:30 – 10:30 | Introduction to AlphaFold and AI-Based Protein Structure Prediction | Lecture |
| 10:30 – 10:45 | Coffee Break | |
| 10:45 – 12:00 | AlphaFold Database: Searching, Retrieving and Downloading Predicted Structures | Demonstration and Exercise |
| 12:00 – 12:30 | Understanding Confidence Metrics: pLDDT and PAE | Lecture |
| 12:30 – 13:30 | Lunch Break | |
| 13:30 – 14:30 | Visualizing AlphaFold Models in PyMOL | Practical Exercise |
| 14:30 – 15:15 | Comparing Experimental and Predicted Protein Structures | Practical Exercise |
| 15:15 – 15:30 | Coffee Break | |
| 15:30 – 16:30 | Limitations, Applications and Further Computational Protein Modelling Tools | Discussion and Demonstration |
Day 5: Final Project – Independent Protein Structure Analysis
Focus: Applying the knowledge and techniques acquired throughout the course to an independent protein modelling project.
| Time | Activity | Format |
|---|---|---|
| 09:00 – 09:30 | Introduction to the Final Project and Project Guidelines | Discussion |
| 09:30 – 10:30 | Selecting a Protein of Interest and Defining the Research Question | Project Work |
| 10:30 – 10:45 | Coffee Break | |
| 10:45 – 12:00 | Retrieving Experimental or Predicted Protein Structures | Project Work |
| 12:00 – 12:30 | Initial Structural Visualization and Exploration | Project Work |
| 12:30 – 13:30 | Lunch Break | |
| 13:30 – 14:30 | Structural Analysis, Identifying Important Residues and Molecular Interactions | Project Work |
| 14:30 – 15:15 | Preparing Structural Images and Project Presentations | Project Work |
| 15:15 – 15:30 | Coffee Break | |
| 15:30 – 16:30 | Final Project Presentations, Discussion and Feedback | Presentation |
Final Project
During the final day, participants will complete a small independent protein structure analysis project using the computational tools introduced throughout the training.
Each participant or group will select a protein of biological interest and perform a structured analysis, including:
- Protein Selection: Identify a protein of interest and formulate a basic research question.
- Structure Retrieval: Find and download an appropriate experimental structure from the RCSB PDB or a predicted structure from the AlphaFold Database.
- Structural Visualization: Import the structure into PyMOL and explore its overall architecture.
- Structural Analysis: Identify relevant chains, residues, secondary structures, ligands, and potential binding sites.
- Molecular Interactions: Investigate selected distances and interactions within the protein structure.
- Model Interpretation: If applicable, evaluate the confidence of an AlphaFold-predicted structure.
- Presentation: Prepare structural visualizations and present the main findings.
Participants will be encouraged to select proteins relevant to their own research interests.
Expected Outcomes
After completing the five-day training, participants will have:
- A foundational understanding of structural biology and computational protein modelling
- Practical experience using PyMOL for protein visualization and analysis
- Experience navigating the Protein Data Bank and AlphaFold Database
- An understanding of AI-based protein structure prediction and its limitations
- Experience with basic structural comparison and molecular interaction analysis
- Completed an independent protein structure analysis project
- Developed the confidence to explore further computational structural biology tools and workflows
Course Details
- Location: Online
- Duration: 5 days
- Format: Online, computer-based practical training
- Level: Beginner to Advanced
- Language: English
- Focus: Structural biology, protein architecture, RCSB Protein Data Bank (PDB), PyMOL, protein visualization, structural analysis, protein–ligand interactions, structural alignment, UCSF ChimeraX, AlphaFold, AI-based protein structure prediction, pLDDT and PAE confidence metrics, and an independent final project
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