DEEdesign
Protein sequences may be designed to fit backbone structures using the Dead End Elimination algorithm, potentially enabling the design of novel proteins with new functions.
Advisor: Chris Bystroff
Participating Students: Yao-ming Huang*, Derek Pitman*, Sasmita Nayak*, Ravi Sood

Protein-Protein Interactions
Protein-protein interactions determine what happens in the cell. A new data structure for protein surfaces has been designed in order to make docking of proteins fast and accurate, and to enable the heirarchical clustering of all protein surfaces.
Advisor: Mohammed Zaki
Participating Students: none

Protein Structure Prediction
Protein structure prediction is being carried out by using Hidden Markov Models to extract sequence-specific knowledge-based potentials for simplified molecules, then running molecular simulations.
Advisor: Chris Bystroff
Participating Students: Patrick Buck*

Protein Design Workshop
Experiment in designing new proteins using MOE and in-house modeling tools. Prerequisites: Knowledge of the Unix environment, programming skill in any language.
Contact: Chris Bystroff

GeoFold
Simplified simulations of protein unfolding using geometric rules allow molecular simulations to extend into the second timescale, one million times longer than the longest molecular dynamics simulations.
Advisor: Chris Bystroff

Game development
ECOME is a model for an evolving food web. The Player chooses prey species and tries to stay alive as all species migrate and evolve. Help develop the front end of this game using graphical interface libraries such as OpenGL. Prerequisites: Knowledge of Fortran95 and basic concepts in GUI programming.
Contact: Chris Bystroff

* indicates students outside the department