Skip to main content
Fig. 2 | BMC Bioinformatics

Fig. 2

From: Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23

Fig. 2

Determination of clustering cutoffs. Top row: example of resulting clusters following the initial native overlap hierarchical clustering step. Each image represents a different cutoff applied for determining the final clusters for that step. These images informed the decision of which cutoff to impose in the final protocol. a Conotoxin and small hairpin clusters at the native overlap cutoff of 0.7, which was ultimately selected as the final cutoff. b At a cutoff of 0.6, the same conotoxin and small hairpin DRPs were assigned to the same cluster despite assuming different secondary structures. c At a cutoff of 0.8, conotoxin DRPs were assigned to separate clusters despite each cluster fold consisting of circular loops and short helical regions. Bottom row: example of a resulting cluster following the knottin reclustering step, with each image representing the knottin cluster containing the most DRPs after applying a different cutoff. Only the disulfide bonds in the DRPs are displayed, in yellow. The cutoffs assessed were (d) 2.0 Å RMSD, (e) 1.5 Å RMSD, and (f) 2.5 Å RMSD. 2.0 Å was selected as the optimal cutoff and used in the final protocol

Back to article page