Using motion planning to compare bound and unbound protein pathways
Description:
The primary goal of this project is to study how pathway accessibility changes in proteins depending on whether they are bound to a ligand or not. This goal is based on the fact that a protein's structure changes when bound to a ligand in order to make it more difficult for the ligand to escape. For this project, we use motion planning to find and compare the accessibility of proteins in their bound and unbound state. The problem can be modeled by using the structure of the protein as the environment and the ligand as a robot to build a roadmap in free space and query for possible paths from the binding site to the surface of the protein. The main features of this project will be to identify proteins in bound/unbound states, to run experiments, and to compare the statistics gathered in order to analyze the changes in path accessibility between bound and unbound states.
I will be using the following databases to identify and gather protein structures for the project.
Final Report