A New Approach for Modeling of Conformational Changes of Multi Chain Proteins

We introduce a new way of modeling conformational movement of multi chain proteins. Several approaches for placing virtual bonds between the chains of proteins were tested. The first one simply connects the first atoms of all chains. The second approach is based on placing the virtual bonds between the most stable parts of the protein. The algorithm can either search for the most stable virtual bonds or the most stable atoms. The last described method performs best. We then compare different approaches among each other and analyze the quality of the geometric structure of the resulting transition pathways.