SUPERFICIAL--surface mapping of proteins via structure-based peptide library design
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Updated: Aug 16, 2026
Overlapping Peptide Library to Map Qa-1 Epitopes in a Protein
Published on: December 20, 2017
Andrean Goede1, Ines S Jaeger, Robert Preissner
1Berlin Center for Genome Based Bioinformatics, 3D Data Mining Group, Institute of Biochemistry, Charité, Monbijoustr. 2, 10117 Berlin, Germany. Andrean.Goede@charite.de
Background:
The determination of protein surfaces and the detection of binding sites are essential to our understanding of protein-protein interactions. Such binding sites can be characterised as linear and non-linear, the non-linear sites being prevailant. Conventional mapping techniques with arrays of synthetic peptides have limitations with regard to the location of discontinuous or non-linear binding sites of proteins.
Results:
We present a structure-based approach to the design of peptide libraries that mimic the whole surface or a particular region of a protein. Neighbouring sequence segments are linked by short spacers to conserve local conformation. To this end, we have developed SUPERFICIAL, a program that uses protein structures as input and generates library proposals consisting of linear and non-linear peptides. This process can be influenced by a graphical user interface at different stages, from the surface computation up to the definition of spatial regions.
Conclusion:
Based on 3D structures, SUPERFICIAL may help to negotiate some of the existing limitations, since binding sites consisting of several linear pieces can now be detected.
