Biochemistry

Recently we developed a method which offers a reasonable solution of sorting the productive/non productive contacts for protein stability. The definition of contacts is based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies.

The stability issue in proteins has quite a large application potential. The method would be useful for wet lab biochemists or structural biologist engineering proteins toward certain functions of structural aspects and solving protein stability issue. The first aim of the thesis is to design a publicly available web tool using the methodology for on-line protein stability guess.

The second aim of the thesis is to use the method for prediction of 3D structures of globular proteins. One of the possible scenarios is a creation of an algorithm which discriminates a great number of examined folds in tertiary structure prediction processes coupled with secondary structure prediction algorithms.