In the second phase of the Help Cure Muscular Dystrophy project, the researchers used a tool called JET which stands for Joint Evolutionary Trees. This tool was used to predict the location of sites on protein molecules which interact or bind with other proteins and compounds. If such sites are important to the proper functioning of an organism, then the gene sequences coding the portions of the protein that correspond to the binding sites are more likely to stay constant (be preserved) as other parts of the gene sequence evolve and mutate over time. The JET tool is used to evaluate the evolutionary changes in the gene sequences of organisms over time to predict the binding sites. By knowing the most likely binding sites, searches to evaluate which proteins and compounds bind most tightly to the protein can be much more focused, thus saving much computation time, as was done for this World Community Grid project. Their paper, published in PLOS Computational Biology, discusses improvements in the JET 2 tool and new strategies for its use to study protein-protein interactions. The researchers plan on using JET2 improvements to help analyze the results from the Help Cure Muscular Dystrophy project.

Paper Title: "Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions"

Authors: Elodie Laine, Alessandra Carbone

Link to paper: http://journals.plos.org/ploscompbiol/article...al.pcbi.1004580.PDF

Prior paper on JET: https://secure.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=75