Given the scarcity of protein-peptide structures and their obvious relevance for drug design, we provide an additional service for peptide design. Since it was recently shown that protein-peptide interactions can be reliably mimicked using interacting fragments from monomeric proteins, it is possible to provide structural variations of peptide ligands using protein fragments. Each ligand peptide in the PepX dataset is associated with its corresponding structural class from the database of protein fragment clusters, BriX. In these fragment clusters, sets of protein fragments with highly similar backbone structure are grouped. Each protein fragment class represents a natural variation on a typical backbone conformation. Mapped on protein-peptide pairs, these structural classes can be used to model and design alternative peptides with slightly adapted backbone conformation that better fit given amino acid sequences.
PDZ domain covered with BriX fragments. To find out more about the covering strategies, check out the video in Related Work.
