Articles and other research material where the PL and OOPS have been used:
- 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
- Recent progress in rapid structure prediction without side-chain searching. Joe DeBartolo, Abhishek Jha, Andres Colubri, Karl F. Freed, Tobin R. Sosnick. Poster presented at the 2006 Midwest Protein Folding Conference. University of Notre Dame, Indiana, USA. May 6, 2006.
- Inverse Protein Folding of Ubiquitin on the Illinois Bio-Grid. Gemmell J, Angulo DS, Sosnick TR, Freed KF, Jha AK, Colubri A, DeBartolo J, Kendall D, von Laszewski G. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL, USA. April 29 2006.
- A realistic statistical coil model for the unfolded state. Abhishek Jha, Andres Colubri, Muhammad H. Zaman, Tobin R. Sosnick, Karl F. Freed. Poster presented at the Gordon-Kenan Graduate Research Seminar: Protein Folding Dynamics. Ventura, California, USA. January 6 - 8, 2006.
- Prediction of Ramachandran Basins using Fragment Libraries. Andres Colubri, Abhishek Jha, Tobin R. Sosnick, Karl F. Freed, R. Stephen Berry. Poster presented at the 4th European Conference on Computational Biology (ECCB). Madrid, Spain. September 28 - October 1, 2005.
- Folding Proteins by Constrained Minimization of a Statistical Potential of Mean Force. Andres Colubri, Abhishek Jha, Tobin R. Sosnick, Karl F. Freed. Poster presented at the 4th European Conference on Computational Biology (ECCB). Madrid, Spain. September 28 - October 1, 2005.
- 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
- Unfolded state webpage: Supplementary material for the article above (unfolded ensembles, Ramachandran maps). A server for generating random coil ensembles is also available.
- AIfold: a Statistical Potential for Protein Folding. Andres Colubri, Jessica Lyn Raddatz, David Angulo. Poster presented at the 12th International Conference on Intelligent Systems for Molecular Biology and 3rd European Conference on Computational Biology (ISMB/ECCB). Glasgow, Scotland. UK. July 31 - August 4, 2004.
- Efficient expansion, folding, and unfolding of proteins. Nelson ED, Grishin NV. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Nov;70(5 Pt 1):051906. Epub 2004 Nov 15. PMID: 15600655
- 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