Team:Thessaloniki/Model
guest@igem:
~/igem/2019/Thessaloniki/Introduction$
modeling_into_lab_assistance --help
–description
The Project’s Model was very helpful for our wet lab, as it provided them with reliable DNA sequences for the circuit, dynamic simulations for questionable DNA systems and theoretical values about the binding affinity.
-result
By modeling the experiments, the team managed to save time and funds, ordering only useful DNA oligos. Furthermore, the binding simulations made the results trustworthy.
guest@igem:
~/igem/2019/Thessaloniki/Introduction$
molecular_dynamics -o BindingAffinity
-q
At the end of the experiment, going back to calculate the binding affinity is not that easy.
-dG
Using Molecular Dynamic Simulations we can calculate the theoretical Gibbs binding energy and compare it with the results.
-Kc
Additionally, using this energy we are able to approximate the equilibrium constant for the binding reaction.
-Read_more
guest@igem:
~/igem/2019/Thessaloniki/Introduction$
genetic_algorithm --make sequence --evaluate
--fill
Finding the best sequences is a bit of black art. Through this algorithm we managed to fill in missing nucleotides for our oligos.
--measure
As each nucleotide could change the characteristics of our system, we tracked down those changes through some evaluation measures. After, we advised those measures to fit in the sequences for our system.
-Read_more
guest@igem:
~/igem/2019/Thessaloniki/Introduction$
system_simulation -i system -o efficiency
-sim
Through fast DNA Stand Displacement simulations, we were able to approximate the efficiency of multiple DNA networks and experiment with them in silico.
--kinetics
Through additional slow simulations we were capable of calculating the kinetic rates of all reactions and provide feedback for calculating backwards the binding affinity.
-Read_more