GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data

The increasing availability of HIV-host interaction datasets, including both physical and genetic interactions, has created a need for software tools to integrate and visualize the data. Because these host-pathogen interactions are extensive and interactions between human proteins are found within many different databases, it is difficult to generate integrated HIV-human interaction networks. We have developed a web-based platform, termed GPS-Prot (http://www.gpsprot.org), that allows users to easily create comprehensive and integrated HIV-host networks including information from public databases and user-uploaded data. A major advantage of this platform compared to other visualization tools is its web-based format, which requires no software installation or data downloads. GPS-Prot allows novice and expert users to quickly generate networks that combine both genetic and protein-protein interactions between HIV and its human host into a single representation. Ultimately, the platform is extendable to other host-pathogen systems.

Biography

Melanie Bennett Brewer is the coordinator for the HARC Center at the UCSF, where she works on web-based systems to integrate and visualize host-pathogen data, using HIV as a model system. She received a Ph.D. degree in Molecular Biology from UCLA in 1993, where she studied the crystallographic structures of diphtheria toxin and first described the phenomenon of “3D domain swapping”, a paradigm for protein assembly that has now been observed in many other systems. Previously, she was a postdoctoral fellow at Caltech, where she studied protein assemblies involved in the iron-storage disorder hereditary hemochromatosis and in Huntington’s disease. Her interests include protein-protein interactions as they relate to normal cellular functioning and pathogenesis and development of systems to integrate and visualize that data.