Research Topic: Expansion of roadmap methods for studying protein folding in order to eliminate the requirement of the native state

Research Goals: Current protein simulations using the probabilistic roadmap method (PRM) need the native structure of proteins to generate new conformations.This limits the number of proteins that can be studied by this method. We explore an alternative way to generate protein conformations (i.e.nodes in the roadmap) by analyzing fragments of the protein rather than the whole protein at once. Ken Dill's group at UCSF has studied these protein fragments using molecular dynamics (MD) simulations. The advantage of this approach is that it does not depend on the native state. We will process their data to generate protein conformations that can then be used in the existing simulation. After implementing the technique, results will be compared to the available experimental data. Tasks :
	        1. Understanding the existing methods for protein simulation  (Week 1 - 2)
			- Reading papers on protein folding and protein kinetics using motion planning
			- Checkout and compile code
			- Learn to run code
			- Find out where the new code will go and create a basic structure for it
		2. Implement the new node generation method  (Week 2 - 5)
			- Write method to read input data and store it  
			- Find out and implement a method to randomly generate phi and psi angles for each residue. 
			- Apply this method to each residue to get the protein conformation	
			- Integrate the method into existing code
		3. Experiments (using Protein G)  (Week 6 - 9) 
			- Determine the distribution of nodes in the funnel
			- Compare the lowest energy conformations generated by this method to the native state
			- Compare the roadmap generated to the existing one (eg. running time, number of nodes required)
		4. Final Project Report  (Week 9 - 10)
	        1. Function to read and store input data			Week 2
		2. Function to generate new conformations of the protein	Week 5
			- Code for individual residue 
			- Code for whole protein
		3. Experimental results						Week 9
			- Distribution of nodes
			- Comparison of conformations and native state
			- Comparison of roadmaps					
		4. Final Report							Week 10