Choose what to redesign

A VHH binds through three loops, its complementarity-determining regions, held on a framework that is much the same across antibodies. Redesigning the loops while the framework stays is the natural first ask: new chemistry at the interface, the fold the scaffold is known for untouched. The 35 residues marked below are the three loops; everything else on chain B, and all of the receptor, is fixed.

The model counts positions along each chain from one; the lab shows the file's own numbering and converts. Everything not marked is written into the request as a fixed position, and a chain that is kept is fixed whole. In the lab you mark residues by clicking the structure or the sequence, dragging a stretch, typing a list, or taking a patch around a landmark; Keep the interface takes a partner's contacts out of the set in one click.

Read more: Phi API: fixed positions