Goals

 

Goal 1:
To acquire an initial list of candidate ICC structures from the Protein Data Bank.

Goal 2:
To establish DNA insert sizes for creating output model files of priority candidates in Pymol. These priority candidates will be used in  GROMACs simulations.

Goal 3:
To successfully use GROMACs software to  run molecular dynamic (MD) simulations on co-crystal designs with expanded DNA struts of varying sizes to determine relative stabilities. From these simulations,  preferred DNA strut expansion lengths can be established for use in laboratory.

Goal 4:
To create educational Pymol videos describing our experimental process.