Quickstart: Protein Design Complete Workflow

This guide walks through creating a complete protein binder design project from scratch as a single workflow.

​

Step 1: Create a New Project

1. From the home page, click “New Project”
2. Enter a project name (e.g., “Designing for external domain of EGFR”)
3. Select “Protein” modality
4. Click “Create”

​

Step 2: Add Your First Target

1. From the project dashboard, click ”+ Add target” in the Targets section
2. Enter target name (e.g., “Target-EGFR”)
3. Choose “Define Sequences” tab
4. Click ”+ Polymer” then “Protein from Sequence”
5. Paste your protein sequence (or import from UniProt)
6. Click “Import” then “Continue”

​

Initialize Target

Complete the 4-step initialization:

1. Verify Unbound Structure - Review the predicted structure

2. Select Crop - Choose region of interest (less than 350 residues ideal)

3. Select Epitope (Optional) - Mark binding site residues

4. Select Flexible Residues (Optional) - Mark flexible regions

Click “Complete Setup” when done.

​

Step 3: Create a Binder Specification

1. Click ”+ Add” in the Binder Specifications section
2. Enter binder specification name (e.g., “Nanobody design V1”)
3. Select “Nanobody” modality
4. Click ”> Continue to Specification”

​

Specify Structure

Choose one:

• Pre-loaded template - Select from provided structures e.g., vWF A1-Camplacizumab Complex
• PDB ID - Import via PDB ID (e.g., 7EOW)
• Upload file - Upload your own structure

​

Select Residues

• All residues are selected by default.
• You can also manually select residues by clicking/dragging
• Recommended: ≤300 residues

​

Configure Design

1. Exclude amino acids (e.g., Cysteine)
2. Create design motifs:
   • Select CDR regions
   • Right-click then “Replace with design motif”
   • For CDR3, specify variable length (e.g., 10-25 residues)
3. Click ”> Create Specification”

​

Step 4: Create an Experiment

1. Click ”+ New Experiment” in the Experiments section
2. Enter name (e.g., “First campaign to find initial hits”)
3. Enter hypothesis (optional but recommended)
4. Click “Create Experiment”

​

Step 5: Run Virtual Screen

1. From the experiment, click “New virtual screen”
2. Enter screen name (e.g., “Small virtual screen to test the setup”)
3. Select “Design (Generative)” type
4. Set budget:
   • Start with 30-100 for a pilot
   • Scale to 10k-100k for production
5. Select your binder specification
6. Select your target
7. Select your experiment
8. Click “Start Protein Design”

​

Step 6: Monitor Progress

While running, you can:

• View progress and elapsed time
• Pause or stop the screen
• Click “View Results in Experiment” to see candidates as they’re generated

​

Step 7: Evaluate Results

Once completed:

1. Review metrics:
   • Top performers binding confidence graph
   • Candidates above threshold counts

2. View candidates:
   • Switch to “Table” tab
   • Filter and select candidates
   • Review 3D structures in the viewer
   • Compare properties (ipTM, pLDDT, binding confidence)

3. Triage:
   • Use thumbs up/down and flags
   • Tag promising candidates
   • Export for experimental validation