Hi,
I've performed I-TASSER over 105 proteins sequences (they are pretty small). These sequences have never been seen before and sadly, template homology models are almost none existent. My C-Scores range from -5 to -1.4 Given the number of sequences, I'm only prepared to invest time into the five sequences which scored between -1.8 and -1.4.
I took these sequences, parameterised them using the Amber FF then performed solvated MD simulations for 500 ns. The smallest of the five sequences also underwent a 1 ms cyclic simulated annealing simulation.
I was wondering what is the best way of 'scoring' a refined structure against the structure returned by I-TASSER? Is there any utility that could possible recalculate the C-Score or TM-Score of a .pdb file rather than just its sequence?
Many thanks
Anthony