Rigidity Analysis of Protein-Ligand Conformations Generated by Molecular Dynamics

Proteins are molecules that flex and bend and perform a multitude of functions in our bodies. Scientists carefully create and design different medicines and drugs in order to regulate disease causing proteins. However there is no current way to visualize how a drug affects a protein on an atomic level. Having methods to visualize this interaction would greatly assist in the drug design and development process. This project uses protein structure data produced by X-Ray crystallography from the Protein Data Bank. Next a freely-available molecular dynamic program takes the protein-drug complex taken from the Protein Data Bank and generates multiple conformations. Using these protein-drug complexes we then use established computational geometry techniques to determine the rigidity of each of the conformations. The final step is to analyze how the rigidity is affected in each of the protein’s conformations. Using this data we can then determine the overall effect the drug has on the protein’s rigidity and flexibility