TCB Publications - Paper Request

Eric H. Lee, Jen Hsin, Marcos Sotomayor, Gemma Comellas, and Klaus Schulten. Discovery through the computational microscope. Structure, 17:1295-1306, 2009.

LEE2009 All-atom molecular dynamics simulations have become increasingly popular as a tool to investigate protein function and dynamics. However, researchers are concerned about the short time scales covered by simulations, the apparent impossibility to model large and integral biomolecular systems, and the actual predictive power of the molecular dynamics methodology. Here we review simulations of proteins with mainly mechanical functions (titin, fibrinogen, ankyrin, and cadherin) that were in the past hotly disputed and also considered key successes. The simulation work covered shows how state-of-the-art modeling alleviates some of the prior concerns, and how unrefuted discoveries are made through the “computational microscope”.



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