Such models capture the essence of the fundamental questions, while being simple enough to enable thorough computational analysis. Using this approach we have demonstrated the usefulness of genetic algorithm for structure calculations. In another study, using another simple model, it was shown that local interactions facilitate folding. This conclusion was recently validated by experimental data about folding rates of small proteins. In another study we suggested a model that explains how evolution could have made the native conformation of proteins to coincide with the conformation with the global minimum of free energy.
Genetic algorithm is a computational paradigm based on biological experience.
We have found it to be a very powerful tool in structural biology applications. The method has been applied to folding of simple models to protein threading and to structure comparison. Proteins are composed of domains that in some cases may have been swapped during evolution. Understanding this process might be useful for protein design. We conduct bio-informatical studies to explore these phenomena in the databases of known proteins.