Use the force

Credit: Opabinia regalis / wikimedia.org" /> Credit: Opabinia regalis / wikimedia.org The paper: V. Hornak, et al., "Comparison of multiple Amber force fields and development of improved protein backbone parameters," Proteins Struc Funct Bioinfo, 65:712-25, 2006. (Cited in 58 papers) The gist: To improve a 25-year-old set of equations, called the Amber force field,

Bob Grant
Bob Grant

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Dec 1, 2008
<figcaption> Credit: Opabinia regalis / wikimedia.org</figcaption>
Credit: Opabinia regalis / wikimedia.org

The paper:

V. Hornak, et al., "Comparison of multiple Amber force fields and development of improved protein backbone parameters," Proteins Struc Funct Bioinfo, 65:712-25, 2006. (Cited in 58 papers)

The gist:

To improve a 25-year-old set of equations, called the Amber force field, which simulate the behavior of complex proteins, Carlos Simmerling, at the State University of New York at Stony Brook, tweaked the parameters that describe protein backbones in the model. The new version of Amber, dubbed "ff99SB," predicts the ways that actual proteins behave in solution.

The impact:

Previous versions of Amber (published in 1999) "were too floppy," says Dave Case of Rutgers University, meaning that they overestimated spontaneous fluctuations in protein structure. "[Ff99SB] is a real quantum leap in terms of the agreement between theory and our observations" with nuclear magnetic resonance (NMR) says Rafael Brüschweiler, at Florida State University.

The...

The future:

Arthur Palmer at Columbia University says that ff99SB simulations have shown movement in tertiary loop regions of ribonuclease H protein from Escherichia coli that have been postulated but never observed. Models such as Amber, may one day be accurate enough to truly predict biomolecular behavior, says Palmer.

"Floppiness" of binase's 109 amino acids
Method Number of "floppy" residues
NMR 3
ff99 (old) 25
ff99SB (new) 3

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