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

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:...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Andrean Goede, Ines S. Jaeger, Robert Preissner
• Keywords: Binding Sites, BMCBI 2005, Non-linear, Proteins