Virtual Screen Budget
Start with a small pilot (30-100 designs) to validate your setup, specifications, and predictions. Once everything looks correct, scale up to 10k-100k designs per campaign—the larger the better, especially for difficult targets or modalities.
Target Selection
Keep target crops under 350 residues for optimal performance. Select epitope residues to guide binding, and mark flexible regions if you expect conformational changes.
Binder Specification Design
For antibodies/nanobodies, focus design on CDR regions. Use variable-length CDR3 (10-25 residues) to increase diversity. Exclude problematic amino acids (e.g., Cysteine) to prevent unwanted interactions.
Candidate Evaluation
Review top performers first by binding confidence, then examine 3D structures to ensure poses are reasonable. Use tags to organize candidates by different criteria (affinity, pose quality, diversity).