Paper Citing NAMD - Abstract
Lee, Eric H.; Hsin, Jen; Sotomayor, Marcos; Comellas, Gemma; Schulten, Klaus
Discovery Through the Computational Microscope
STRUCTURE, 17:1295-1306, OCT 14 2009
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 that were in the past both hotly disputed and considered key successes, namely of proteins with mainly mechanical functions (titin, fibrinogen, ankyrin, and cadherin). 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. "
