The scientific community considers protein folding as one of the most significant challenges in science and engineering, that has broad economic and scientific impact, and whose solution can be advanced only by applying high performance computing techniques. To achieve the performance of the order of quadrillion calculations per second for each processor, IBM initiated to build a supercomputer, BLUE GENE, a successor to Deep Blue, on September 11,2000.The system will be simple, ultra speed, self healing and will be able to handle more than 8 million threads of computation simultaneously. BLUE GENE will consist of more than 1 million processors, each capable of one billion operations per second (1 gigaflop).32 of these processors will be placed on a single chip(32 gigaflops).A compact 2 feet board containing 64 of these chips, will be capable of 2 teraflops, making it as powerful as the 8000 suare feet ASCI computers. BLUE GENE will help to solve the enormously complex protein folding mystery, that will have profound implications for understanding diseases, genetic engineering and designing more effective drugs.