Abstract
THE SUPERCOMPUTER Anton is online and ready to fold proteins. D. E. Shaw Research, which designed and built the massively parallel Anton, has at last verified the machine’s much-publicized capabilities, reporting Anton’s first major long-time-scale protein dynamics simulations. The computer performed two types of simulations of well-studied systems: In the first, Anton’s 100-microsecond simulations of the protein domain FiP35 show that the domain folds and unfolds in the same progression of steps each time—a surprise to some researchers. The second simulation involved a longer, one-millisecond study of the dynamics of the already folded protein bovine pancreatic trypsin inhibitor (BPTI), which explored the intricate motions of protein in water. Results were published in Science ( 2010, 330, 341). “This work demonstrates that their machine really can do the tasks they proposed,” says Vijay Pande, an associate chemistry professor at Stanford University and creator of the folding@home project, which harnesse...
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