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Open Access Software

SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design

Andrean Goede*, Ines S Jaeger and Robert Preissner

Author Affiliations

Berlin Center for Genome Based Bioinformatics, 3D Data Mining Group, Institute of Biochemistry, Charité, Monbijoustr.2, 10117 Berlin, Germany

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BMC Bioinformatics 2005, 6:223  doi:10.1186/1471-2105-6-223

Published: 9 September 2005

Abstract

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.