When the University of California wanted the capability to visualize its new Ebola Genome Browser in 3-D, they knew exactly who to call: Rachel Karchin at The Johns Hopkins University’s Institute for Computational Medicine.
In 2013, Karchin and her team produced a Web application that displayed changes in DNA that were possibly important to human disease and projected them onto the 3-D structure of proteins. Called the Mutation Position Imaging Toolkit (MuPIT), the application allowed biologists to explore potentially significant changes. The University of California wanted the same capability for Ebola proteins.
“The Ebola Genome Browser displays information in a linear view, but it’s interesting to see it in the context of a 3-D protein,” says Karchin, an associate professor of biomedical engineering.
The Ebola Edition of MuPIT connects with the Ebola Genome Browser to display detailed genetic information about the virus in 3-D. Users can zoom in and out, turn the protein around and upside down, and map specific mutations.
The goal of the free, publicly available toolkit is to shed light on new targets for preventive treatments for Ebola virus disease infections. Karchin hopes the application will make it easier for biologists to interpret the functional implications of mutations, the mutations’ relationship to Ebola virus evolution and the virus’ potential vulnerabilities.
“Researchers are continuing to collect blood samples from people who have Ebola and sequence the virus,” says Karchin. “We will continue to update these new mutations in our system.”