Empirical Energy Functions
During the docking of two proteins conformational changes can be observed ( induced fit ). Especially in the active site of a protein amino acid sidechains change their conformation. In this research work molecular mechanics force fields (like AMBER) are used to score these conformational changes.
In a first step synthetic conformations are build by rotating the amino acid sidechain torsion angles (CHI angles). For each conformation the potential energy is calculated using the AMBER force field. Then a search of the energetic best conformations has been performed. We recieved a distribution of the torsion angles for each aminoacid type. At the moment only one torsion angle is modified at a time. We plan to develop a model to perform conformational changes on the whole sidechain at once.
This project is supported by the DFG graduate program