Paper Citing NAMD - Abstract
Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida
Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement
PHYSICAL REVIEW E, 79 Art. No. 060901, JUN 2009
A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.
