Different ab initio 3D structure prediction for same protein sequence by trRosetta

Question

[saamar.rajput]

I used trRosetta tool to predict the 3D structure of my protein from amino acid sequence, I did this twice to see if trRosetta predicted the smae 3D structure. Unfortunately the 3D structure was different for the same sequence, could someone explain why this could be or if I am doing something wrong? or if someone could refer a nice tool that does ab initio 3D structure prediction?

Answer 1

[jgreener]

Have a read of the trRosetta paper and the section "Structure Determination by Energy Minimization with Predicted Restraints" will give you more information on the variability.

Of course, that doesn't rule out you having made a mistake. Perhaps look at the degree of variability: are you talking 2 Å or 20 Å RMSD difference between the models? What happens when you model the sequence 10 times?