%0 Journal Article
%T SuperMimic ¨C Fitting peptide mimetics into protein structures
%A Andrean Goede
%A Elke Michalsky
%A Ulrike Schmidt
%A Robert Preissner
%J BMC Bioinformatics
%D 2006
%I BioMed Central
%R 10.1186/1471-2105-7-11
%X SuperMimic identifies compounds that mimic parts of a protein, or positions in proteins that are suitable for inserting mimetics. The application provides libraries that contain peptidomimetic building blocks on the one hand and protein structures on the other. The search for promising peptidomimetic linkers for a given peptide is based on the superposition of the peptide with several conformers of the mimetic. New synthetic elements or proteins can be imported and used for searching.We present a graphical user interface for finding peptide mimetics that can be inserted into a protein or for fitting small molecules into a protein. Using SuperMimic, promising locations in proteins for the insertion of mimetics can be found quickly and conveniently.Many protein interactions are known, mostly involving other proteins, peptides or different organic molecules, and more and more are being deciphered. The main goal of drug design is to interfere specifically with these interactions. As peptides are often poor drug candidates, the need arises for bioequivalent compounds with better pharmacological properties. Starting from a known spatial structure, the aim is to find compounds that mimic the function of a peptide but have improved cellular transport properties, low toxicity, few side effects and more rigid structures as well as protease resistance [1,2].Various methods exist for developing peptide mimetics. These include computational as well as experimental screening methods. One method is to identify small peptides that are essential for the interactions of the protein, e.g. using SPOT synthesis. Subsequently, mimetics for these peptides are designed that can be used as drugs. On the basis of a known protein structure, scaffolding templates for binders can also be constructed and then optimised using different methods (see [3-5] for reviews).The approach presented in this paper is to detect peptide mimetics directly using a known protein structure and a mimetic structure
%U http://www.biomedcentral.com/1471-2105/7/11