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Discovery through the computational microscope.

ABSTRACT: 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."

SUBMITTER: Lee EH

PROVIDER: S-EPMC2927212 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

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Discovery through the computational microscope.

Lee Eric H EH Hsin Jen J Sotomayor Marcos M Comellas Gemma G Schulten Klaus K

Structure (London, England : 1993) 20091001 10

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 mechan ...[more]

PMID: 19836330

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