# Motif Scaffolding

Protein motif scaffolding usually fixes both where a motif sits along the chain and the relative pose of several rigid fragments, yet many applications supply neither. NomadFlow takes each motif group as a condition, holds each group's internal geometry exactly with a group projection, and lets the groups move independently through the first half of generation before locking them as conditioning to complete the scaffold. On 21 multi-group tasks adapted from Protpardelle, 19 reach unique success; against the same residue set fixed as one rigid body, the median ratio is 0.57 in yield and 1.00 in unique successes.

Protein motif scaffolding usually fixes both where a motif sits along the chain and the relative pose of several rigid fragments, yet many applications supply neither. NomadFlow takes each motif group as a condition, holds each group's internal geometry exactly with a group projection, and lets the groups move independently through the first half of generation before locking them as conditioning to complete the scaffold. On 21 multi-group tasks adapted from Protpardelle, 19 reach unique success; against the same residue set fixed as one rigid body, the median ratio is 0.57 in yield and 1.00 in unique successes.