Parallel processor opens up genomics data
BioServer, designed to overcome one of the primary obstacles to
drug discovery - taking the huge amount of data coming from
genomics efforts and applying it to the design of new drugs.
The company reports that BioServer can successfully calculated the binding energy of protein and drug candidates with unprecedented accurately and at high speeds.
This success confirms the potential of in silico drug design and will accelerate the development of new therapeutics, according to Fujitsu.
Research conducted in a laboratory is mostly done by analysis based on actual experimentation, which entails costly reagents and testing equipment. Applying computer simulation to focus on an area of experimentation prior to the testing phase can save time and money.
However, since proteins are large molecules consisting of tens of thousands or even millions of atoms, a staggering amount of computing time is required to calculate their complete structure. This calculation time can be reduced by making partial calculations and simplifying the target molecule, but accuracy and the usefulness of the results are often decreased.
Fujitsu has sought to address these problems through the development of its massively parallel simulator. The BioServer can combine up to a total of 1,920 CPUs in a single rack just two feet wide, three feet deep and 6.5 feet high. Each of the processors simultaneously executes a simulation program that models a protein's structure and binding characteristics.
By having each processor operate independently, and in parallel to calculate the model under different conditions, the BioServer is able to quickly produce highly precise simulations.
The individual CPUs in the BioServer are from Fujitsu's FR-V series of embedded processors, which use the Very Long Instruction Word (VLIW) architecture based on the company's supercomputer technology. The power consumption of the CPU, however, is only one-fiftieth of a typical processor used in a PC. The machine runs the axLinux operating system from Axe.
"In one stroke, the BioServer gives us access to 2000 times the calculating power of the desktop computers we have been using, removing a bottleneck on drug design and making the development of new compounds exceedingly more efficient," said Masayuki Mitsuka, director of business development at Zoegene, which has been carrying out validation tests on the system.
The results of this testing were presented at the International Conference on Biological Physics 2004, held in Sweden in August.
