The new resource extends ongoing efforts in proteomics at SDSC and the University of California, San Diego (UCSD), and will enable the emerging science of structural genomics, considered the "next wave" of biology. Ultimately, the project will improve protein engineering and design with potential societal impact ranging from improved food production to toxic waste clean-up to drug design.
"This is the era of structural biology as manifest in the various structural genomics projects underway worldwide", stated Philip E. Bourne, principal investigator of the project and director for Integrative Biosciences at SDSC and professor of pharmacology at UCSD. "With protein structures at centre stage comes the need for further structure and sequence characterisation, more informed decisions about which new structures to determine, and the need for new tools to associate sequence, structure, and biological function."
Currently, protein sequence information is being produced at such a rate that discovering protein structure and biological function has lagged far behind. Structural genomics, high-throughput structure analysis of as many open reading frames as can be determined in a given genome, is starting to have an impact to address this problem. The SPAM project will take scientists to the next step of understanding biological function by applying this new wealth of structure data.
SDSC and National Partnership for Advanced Computational Infrastructure (NPACI) Director Francine Berman noted: "This is a very exciting project for SDSC, not only does it bring our computational science infrastructure to bear on a problem of great significance and for which we have significant expertise, it also forges new collaborations with our sister institutions, the Burnham Institute and the Keck Graduate Institute."
One task of the resource, to use and develop new algorithms, will be to take the near-exponential growth of protein sequence information and run it through a pipeline to assign putative functional annotation and model structures where no experimental structures exist. "The collaboration supported by this funding allows us to build on our ability to predict protein structure from the linear genetic alphabet", explained Adam Godzik, director of bio-informatics and structural biology at the Burnham Institute. The results will be stored in a database for worldwide community access through the Web.
"One of the strengths of this effort is that it brings together a group of individuals from different institutions with distinctly different but complementary expertise to develop and implement a range of computational tools in structural genomics", stated T. Gregory Dewey, director of research and professor at Keck Graduate Institute. "We anticipate a lot of synergy on this project resulting from this focused collaboration."
"Already we are moving towards the next step", added Dr. Bourne. "SPAM forms a kernel for a larger integration effort bringing together the many resources that we and others maintain on the role of proteins in living systems. Our long term goal is to establish what we call the Encyclopedia of Life, a reference point for information on life's building blocks of use to everyone who is curious enough to ask the question: how does it work?"
Co-investigators with Philip Bourne on SPAM are Adam Godzik, director of bio-informatics and systems biology at the Burnham Institute; Ilya N. Shindyalov, senior staff scientist at SDSC; T. Gregory Dewey, professor and director of research, and David Wild, director of computing and associate professor at the Keck Graduate Institute in Claremont, California.
The Burnham Institute, founded in 1976, is an independent, non-profit, public benefit organisation dedicated to basic biomedical research. Since 1981, the Institute has earned designation from the National Cancer Institute as a basic-science Cancer Center. In 1999, the Institute established the Del E. Webb Center dedicated to research on neurodegenerative diseases and aging.
Keck Graduate Institute of Applied Life Sciences was founded in 1997 with a $50 million challenge grant from the W.M. Keck Foundation. It is the first American graduate school dedicated exclusively to the applied life sciences. KGI's mission is to pursue educational programmes and research aimed at translating into practice, for the benefit of humanity, the power and potential of the life sciences.