Research overview

We are interested in learning physical principles and microscopic details in protein folding, stability and interactions. How and to what extent do electrostatic interactions modulate protein stability and folding? What are the origin, feature, and effects of the denatured-state interactions? Can we quantify hydrophobic effects? What is nature's design principle for increasing thermo stabilities of proteins? From a practical standpoint, our goal is to contribute quantitative knowledge for engineering proteins with desired stability and function, and for designing strategies to overcome the drug resistance problem.

Towards these goals a current focus of the lab is to develop theoretical methods and computer simulation tools to significantly advance fundamental understanding and quantitative prediction of electrostatic contributions to protein folding, stability and interactions. Specifically, we are further developing the constant pH molecular dynamics technique to enable fully atomistic studies of pH-dependent conformational phenomena and more accurate electrostatic calculations for proteins and nucleic acids. We are combining new simulation approaches, analytical theories, and experimental data to offer residue-specific characterization of protein unfolded states. Finally, we are interested in creating new computational tools for solving problems of interest to detergent and biotechnology industries.

News & Highlights


Dec 2011 - A tutorial of constant pH molecular dynamics is published on google site and YouTube

Dec 2011 - Jason won a Chemical Computing Group Excellence Student Travel Award to attend the spring 2012 ACS meeting in San Diego. Congratulations! Well done!

May 2011 - Jason received Astellas Pharma Award for outstanding graduate research achievements. Congratulations, Jason! Well deserved!!!

April 2011 - Jason won a travel scholarship to present his work in American Conference on Theoretical Chemistry in Telluride.

March 2011 - Dr. Shen received the National Science Foundation CAREER award.

Oct 2010 - Porphyrin paper highlighted in JACS Select #9: Interface and Inorganic Chemistry and Biology.
                See Adam's orbital diagram chosen as the cover page of the issue!

Feb 2010 - Dr. Shen received American Chemical Society HP Outstanding Junior Faculty Award.

Nov 2009 - CCB lab was awarded 200,000 SU of computing time from TeraGrid.

Feb 2009 - Students from the CCB class participated in the first worldwide blind prediction of protein pKa's.

Sept 2008 - Research from University of Oklahoma in enzyme research provides new insights.

Feb 2008 - "Exceptional" paper, evaluation on "Faculty of 1000 Biology"

Oct 2007 - Papers of the week: A new alternative "endosomic" amyloid hypothesis.

Oct 2007 - News and Views from the Scripps Research Institute: The Goldilocks Scenario..