AndrewSymes (Talk | contribs) |
|||
Line 52: | Line 52: | ||
<p> | <p> | ||
− | 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 | + | 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 make informed decisions on the modification of their proteins. |
+ | |||
</p> | </p> | ||
Line 67: | Line 68: | ||
<br> | <br> | ||
<b>The RMSF data</b> 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. | <b>The RMSF data</b> 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. | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
</p> | </p> | ||
<div class="header-area"> | <div class="header-area"> | ||
− | |||
<div class="header-area"> | <div class="header-area"> | ||
− | <h1> | + | <h1>Access</h1> |
− | <h2> | + | <h2>How to access iGAM</h2> |
</div> | </div> | ||
+ | <p>To access the iGAM tools please visit https://github.com/ReverendSymes/iGAM and download the R package project.</p> | ||
<p></p> | <p></p> | ||
Revision as of 00:57, 22 October 2019
Inspiration
What needs to be addressed?
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 make informed decisions on the modification of their proteins.
https://github.com/ReverendSymes/iGAM
iGAM
the international genetic algorithm machine
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.
Access
How to access iGAM
To access the iGAM tools please visit https://github.com/ReverendSymes/iGAM and download the R package project.