The modification of proteins can often be a daunting ordeal. For each single amino acid change there are 23 different possibilities to be considered. iGEM Calgary has generated a toolbox to allow iGEM teams to generate their own genetic algorithms make informed decisions on the modification of their proteins. iGAM, the international genetic algorithm machine was developed to assist iGEM teams in squeezing every ounce of utility out of their proteins.

To assist in the dynamic characterization by other teams we looked to develop a methodology that allows for the calculation and aggregation of Brownian motion measurements for each amino acid in a sequence. The Brownian motion measurement chosen was the Root Mean Square Fluctuation(RMSF) calculated for every atom of a protein in ten picosecond intervals.

The RMSF data was calculated from a nanosecond Molecular Dynamic Simulation(MDS) completed within GROMACS, an industrial MDS software. These values were then averaged over each amino acid, this ensured that the unit of measurement was observed on a scale that was modifiable by teams. This resulted in a series of curves that quantitatively expressed the dynamics for each amino acid.