D.E. Shaw Supercomputer Sets Protein-folding Record

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According to this story at Nature News, a specially designed supercomputer named Anton has simulated changes in a protein’s three-dimensional structure over a period of a millisecond — a time-scale more than a hundred-fold greater than the previous record.

Named after after Antonie van Leeuwenhoek, the seventeenth-century father of microbiology, Anton was created at D.E. Shaw Research, an independent research institute in New York founded by David Shaw, formerly a professor at Columbia University in New York.

Anton’s simulations are based entirely on physical models of the forces among atoms in the protein and its surrounding water molecules. The computer divides time into tiny steps, each perhaps a femtosecond long, and determines how the atoms will move in each period by calculating the forces between all the pairs of atoms in the system. Understanding those movements could be critical for understanding basic cellular processes, and for designing drugs that target particular protein conformations, says Eliezer. Proteins may become unfolded before they are degraded, for example, or when they are prepared for transport across a cellular membrane. And proteins that are not properly folded can cause diseases such as cystic fibrosis and Alzheimer’s disease.