SuperMimic is a tool for conformer based fitting of peptide mimetics into protein structures.Many protein recognition mechanisms, mostly involving other proteins or peptides, are known, and more and more of them are being deciphered. To intervent these interactions is the main goal of drug design. As peptides are often poor drug candidates, the need for bioequivalent compounds with better pharmacological properties arises. Starting from a known spatial structure, the goal is to find compounds that mimic the function of a peptide while obtaining improved cellular transport properties, stable structures and resistance against proteases.
The approach used in the program SuperMimic is to identify peptide mimetics starting from a known protein structure and conformations of a mimic, which are spatially superposed with the protein backbone. A compound library with peptidomimetic compounds collected from the literature as well as several protein structure libraries are provided, which can be scanned exhaustively.
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SuperMimic – Fitting peptide mimetics into protein structures
Reviewed by Andrean Goede, Elke Michalsky, Ulrike Schmidt, and Robert Preissner
BMC Bioinformatics. 2006; 7: 11.