The purpose of Scaffold Select is to help identify proteins that would make good scaffolds for the design of epitope-binding proteins. The protocol performs searches through a protein-peptide database looking for peptides which have high sequence similarity to the target epitope. The proteins which bind the peptides that match the target sequence either exactly or are chemically very similar are returned as potential scaffolds for design. Scaffolds are ranked according to a scoring algorithm which considers the percent identity, and the amount of burial of residues in the match.

For more information, please see the publication:
A Structural Bioinformatics Approach For Identifying Protein Scaffolds Predisposed to Bind Preselected Target Proteins
Choi, E.J., Jacak, R., and Kuhlman, B. (submitted)

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