The Toyota Technological Institute at Chicago is awarded a grant to develop a long-term sustainable web server for low-homology protein threading by making use of the NSF-sponsored cyberinfrastructure Open Science Grid (OSG). The OSG has been proved to be very useful in many research areas including protein folding, protein docking, geoscience and particle physics . The specific goals of this research are: (1) To develop a public protein threading web server that can thread a single protein sequence to the whole template database within minutes and thus, provide service to a large number of users. The server will use OSG, which can easily distribute millions of jobs to the supercomputers around USA, as the back-end computing engine so that our server can run jobs on thousands of CPUs free of charge and we can also easily maintain the server in the very long term beyond the funding period of this project at almost no cost. (2) To customize the web server specifically for low-homology protein threading by incorporating a profile-entropy dependent scoring function into the server. The server will significantly improve modeling capability of low-homology proteins, for which existing protein modeling programs cannot generate good models. The server developed by this project will help both individual biologists and experienced bioinformatics teams analyze the structure and function of proteins without solved structures, especially those low-homology proteins from metagenomic data. This protein modeling web service will ultimately benefit the public by providing a necessary infrastructure for applied areas of study such as alternative energy sources and new medicines.
By developing a long-term sustainable web server empowered by the OSG, this project will promote the application of the NSF-sponsored cyberinfrastructure to scientific research. The development, implementation, and evaluation of the whole project will also promote the timely and effective knowledge dissemination related to structure bioinformatics and distributed/grid computing and will train students in both basic biological sciences and advanced computing techniques.
