As a research fellow at the University of Chicago from 2002 to 2005, I studied the protein folding problem. This problem consists in predicting the three dimensional structure of a protein molecule given the only information of its linear sequence of amino acids. This research was conducted in a highly multidisciplinary and collaborative environment, with experts from molecular biology, computer science and physical chemistry.

I help to design algorithms and models to simplify the huge complexity of protein molecules, while trying to keep the accuracy of the predictions. Based on these algorithms, I implemented a set of libraries and tools to simulate protein folding on computer clusters. Even though I am not formally associated to the University of Chicago anymore, the project continues to this day. Several graduate students are currently using the software to derive new results and to improve the original algorithms. The original website of the project is available here (with links to the simulation and visualization tools I developed):
http://protlib.uchicago.edu
The website with updated information about the ongoing research is the following:
http://godzilla.uchicago.edu/

The following are some research articles that I have authored and co-authored on this topic:

• Mimicking the folding pathway to improve homology-free protein structure prediction. DeBartolo J, Colubri A, Jha AK, Fitzgerald JE, Freed KF, Sosnick TR. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3734-9. Epub 2009 Feb 23. PMID: 19237560. Supplementary info.
  
• Reduced Cb statistical potentials can outperform all-atom potentials in decoy identification. Fitzgerald JE, Jha AK, Colubri A, Sosnick TR, Freed KF. Protein Sci. 2007 Oct;16(10):2123-39. PMID: 17893359
• Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding Simulations. Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF. J Mol Biol. 2006 Nov 3;363(4):835-57. Epub 2006 Aug 18. PMID: 16982067
• Statistical coil model of the unfolded state: resolving the reconciliation problem. Jha AK, Colubri A, Freed KF, Sosnick TR. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13099-104. Epub 2005 Aug 30. PMID: 16131545
• Helix, Sheet, and Polyproline II Frequencies and Strong Nearest Neighbor Effects in a Restricted Coil Library. Jha AK, Colubri A, Zaman MH, Koide S, Sosnick TR, Freed KF. Biochemistry. 2005 Jul 19;44(28):9691-702. PMID: 16008354
• Prediction of Protein Structure by Simulating Coarse-grained Folding Pathways, a Preliminary Report. Colubri A. J Biomol Struct Dyn. 2004 Apr;21(5):625-38. PMID: 14769055