Modeling protein interactions is widely used in modern biomedical sciences. With the extreme interest to the protein problem it is crucial to mathematically describe protein interactions.; There are two major approaches to the protein docking problem: consider a protein as a rigid body, or allow a protein some flexibility. This work represents the second approach: we allow certain sidechain (and, also, ultimately portions of the protein backbone) to exhibit a certain degree of flexibility. We focus on interactions within one protein (the single protein problem models the same binding process as in protein-protein interaction, with the only difference being that the binding regions come from one macromolecule instead of two). In our problem we will use a hybrid approach combining a distributed search technique and a continuous optimization technique.
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