Projects

Project Submission Guidelines

Students in the course will be required to do a final project. We have helped you pick a topic, something you are interested in, and in a typical project, you will (a) implement, (b) analyze, (c) improve, (d) extend, or (e) apply (often more than one) the concepts from your chosen field.
For the submission of the final project, everyone is required to submit a 7-10 page final project report. The report should contain background information with appropriate references, should clearly state the problem, methods and results. If you will write code for your project, zip it and submit that along with your project report. Your final report should be a PDF from pdflatex, and we encourage you to include illustrative pictures and figures in your report.
Please indicate clearly if there is unpublished data in your report and we will take appropriate measures to protect it.
Please email your project report to your TA no later than May 6th, 2011.

Presentation Schedule

Date	Presenter	Topic	Reading
March 30, 2011	Pablo Gainza-Ciraqui	Belief Propogation and Protein Design Slides	Chapter 25
April 1, 2011	Swati Jain	Normal Mode Analysis. Slides	Chapters 21-23
April 6, 2011	Mark Hallen	Dead-End Elimination with Backbone Flexibility - BRDEE and DEEPer.Slides	Chapter 12
April 8, 2011	Samuel Ramirez	Ensembles Slides	Chapters 12,24
April 13, 2011	Chittu Tripathy	Pool - Algorithm for Protein Loop-Closure Slides Paper	Chapters 15,16,17.1,18.1
April 15, 2011	Chetan Rupakheti	Dead-End Elimination for Inhibitor Design Slides PyMOL Movie	Chapters 11-12
April 20, 2011	Sterling Dorminey	Distance Geometry Slides	Chapters 31-32
	Victoria Arendt	Peptide Design Slides	Chapter 9
April 22, 2011	Tanya Mitropoulos	NMR - NOESY and Symmetric Proteins Slides	Chapters 2,3,8,17.5,18.1.4
	Carrie Ho	NRPS and SVM Slides	Chapters 10,12,27-28,46

For days with one talk: Talk Time - 50 mins, Questions -10 mins
For days with two talks (April 20, 22): Talk Time - 20 mins, Questions - 10 mins