Dr. Pang at the Mayo Clinics is using his very own supercomputer to run his Computer-Aided Molecular Design Laboratory (CAMDL) in hopes of discovering new ways to fight infections and beat cancer.
CAMDL specializes in developing computer simulated models aimed at the discovery of new treatments for infectious diseases and cancer. It is one of few labs conducting advanced research in computational, medicinal, synthetic and combinatorial chemistry under one roof.
The laboratory houses supercomputing hardware and software used to process highly complex biological data, and develop comprehensive databases of three-dimensional molecules. Dr. Pang has adapted his imaging concepts from the small computer screen to a large wall screen where visitors are drawn into a three-dimensional, sub-microscopic world. Researchers can examine and study, in simulation, microsecond-scale proportions of proteins and enzymes associated with malaria, avian flu and severe acute respiratory syndrome (SARS). This ability has led to significant discoveries in the lab that Dr. Pang says will impact the prevalence and spread of infectious diseases.
Dr. Pang has developed a 3-D model of neuraminidase (NA) of the H5N1 virus. He found that the conformation (shape) of the inactive, monomeric NA of the H5N1 virus is very different from the conformation of the active, tetrameric NA of the H5N1 virus. He proposed that small molecules that stabilize the monomeric NA can disrupt the tetrameric NA and thereby inhibit NA of H5N1. This opens a possibility to use multiple antiviral agents that could simultaneously target multiple forms of the NA molecule to minimize the resistance problem of current anti-influenza drugs.
The CAMDL computing system is a terascale system, one the most powerful available. Terascale measures computational power in teraflops, or floating point operations per second, and is capable of processing one trillion calculations per second. CAMDL consists of two terascale systems of 1,060 processors that have been strung together for a combined power of 3.8 teraflops, which reflects teraflop power per user or research group. Dr. Pang is pushing toward faster computer systems and within two years, hopes to have achieved petaflops status, equivalent to 1,015 teraflops or 1,000 trillion floating-point operations per second.
“Our supercomputer is just a Strad (a Stradivarius violin): whether the sweet music can get out of this instrument is largely dependent upon the player,” says Dr. Pang.
It would take Dr. Pang 20 days to complete a simulation of a protein structure using the terascale systems he built as compared to the same simulation using a single conventional desktop computer which would take about 28 years.