I use RosettaDock to find the binding site of the proteins. The structure is solved by NMR.
I use the default option:
in:files:s vegf_vegf.pdb -docking:randomize1 -out:nstruct 1000 -out:file:o vegfdimer
I did twice with the same option and the same pdb file, but the result is different.
The first one is right. The second is wrong. I don’t know what is the reason?
It seem that it is not reproducible.
I search the forum to fine some answers.
1. NO other data: lowest score = best result
2. Experimental hints: Using those to figure out which model is most likely to be accurate
Why I have the different result with the same initial condition?
How can I confirm that the protein really search the whole surface of the other protein?
How the program move one of the protein to the surface?
Dose it make a latitude and longitude lines on the protein?
Thanks for reading this.