Besray Unal

PhD, computational Science and Engineering, Koc University

eunal@ku.edu.tr

Rational Peptide Design

The computational inhibitor design focus is currently changing from small molecules to peptides.

As the research in the area is recent, there is not enough data about the high-quality rational design methods,

the properties of superior peptide inhibitors, or the limits for the binding energy of peptide inhibitors

to their target proteins. My projects investigate the common properties of peptide inhibitors and determine

novel strategies for the peptide design problem. First specifically, the known peptide inhibitors are examined and their

entropic, energetic properties are determined; the information of protein data banks is studied in order to

determine the thermodynamic properties of the known protein sequences.

Novel peptides are designed for target proteins. The design of peptides is accomplished by employing Genetic and Viterbi.

algorithms. The computational search for interaction affinity between the protein and the peptide is done via molecular docking tools;

AutoDock and GOLD. Up to date via applying our algorithms, we are able to design peptides that selectively bind to

Fibroblast Growth Factor Receptor, NFkB, and Erythropoietin proteins. The techniques are being applied to other protein

models. We would like to design peptides that can either act as inhibitors or that can be used in biotechnology area.