We have created the design pipeline from Protein Hunter, Boltz-2, and custom ranking algorithm
- Extract the nanobody scaffold from the available structure (7TXZ) together with the contact residues of target protein G.
- Run iterative hallucination approach with Protein Hunter (Boltz-2 version) to refine CDR3 regions by fixing FR regions
- Estimate iPTM, iPSAE and Pyrosetta scores including dSASA and interface_hbonds and calculate the combined scores with the inverse weights
• pTM: 1
• ipTM: 1
• iPAE: 1
• dSASA: 2
• hbonds: 2
- Rank the sequences based on custom scores to shortlist the designs
- Cluster the sequence similarity of CDR3 regions and choose the one with highest ipSAE from each distinct cluster
- Rank top 10 from custom scores + ipSAE
