Getting Started Tutorial

Prerequisites

Before starting, ensure you have:

• Access to Amazon Bio Discovery (AWS account or SSO credentials)
• A target protein structure file (PDB format)
• Basic understanding of antibody design concepts

Step 1: Create Your First Project

1. Sign in to Amazon Bio Discovery
2. Navigate to the Projects section
3. Click "Create Project"
4. Fill in the project details:
   Name: "My First Antibody Project" Description: "Learning to use Amazon Bio Discovery for antibody design" Objective: "Generate antibody candidates against target protein X"
5. Click "Create" to save your project

Step 2: Upload Your Target Structure

1. Open your newly created project
2. Navigate to the Files section
3. Click "Upload Files"
4. Select your PDB file or drag and drop it
5. Wait for the upload to complete and validate

Step 3: Select a Recipe

1. Go to the Experiments section
2. Click "Create Experiment"
3. Choose "De Novo Antibody Generation" from hosted recipes
4. Review the recipe description and modules included
5. Click "Select Recipe"

Understanding Recipes

Recipes are pre-built workflows that combine multiple computational modules:

• Design Modules: Generate new antibody sequences
• Score Modules: Evaluate antibody properties
• Analysis Modules: Process and rank results

Step 4: Configure Your Experiment

1. Name your experiment: "First Antibody Design Run"
2. Select your uploaded PDB file as the target
3. Configure key parameters:
   • Number of designs: 100 (good starting point)
   • Target chain: Select the appropriate chain
   • Framework: Choose human framework
4. Review the cost estimate
5. Click "Configure Experiment"

Step 5: Run Your Experiment

1. Review all experiment settings
2. Confirm the cost estimate
3. Click "Run Experiment"
4. Monitor progress in the experiments dashboard
5. Receive notification when complete (typically 30-60 minutes)

While You Wait

Experiment runtime depends on complexity and parameters. Use this time to:

• Explore other recipes and modules
• Read best practices documentation
• Plan your next experiments

Step 6: Analyze Results

1. Navigate to your completed experiment
2. Click on the "Results" tab
3. Explore the candidate antibodies:
   • View in table format for detailed properties
   • Use visualization tools for structure analysis
   • Apply filters to identify top candidates
4. Use AI recommendations to guide selection
5. Download results for further analysis

Key Metrics to Evaluate

• Binding Affinity: Predicted KD values
• Developability: Manufacturing and stability scores
• Specificity: Off-target binding predictions
• Immunogenicity: Risk assessment scores

Step 7: Next Steps

Iterate and Optimize

• Adjust parameters based on initial results
• Try different recipes or modules
• Incorporate experimental feedback

Wet Lab Validation

1. Select your top 5-10 candidates
2. Navigate to "Send to Wet Lab"
3. Choose appropriate assays and conditions
4. Submit order to wet lab partner
5. Track progress and receive experimental results

Congratulations!

You've successfully completed your first Amazon Bio Discovery experiment. You now have:

• A project for organizing your work
• Experience with the experiment workflow
• Computational antibody candidates
• Understanding of the results analysis tools