Protein RNA docking

Question

[monu46010]

Hi,

I am bit confused about the difference between bound and unbound docking. What initial structures are used in both cases of docking?

Thanks
Mn

Answer 1

[João Rodrigues]

This is a case where reading virtually any publication in the docking field will give you an answer in the methods section.

Regardless, bound docking usually means the initial structures come from the structure of the complex, usually experimentally determined. Unbound, on the other hand, means the initial structures come from structures of the same protein/RNA/DNA molecule that were determined in isolation.

In practice, bound docking is easier because you already have the right conformations for the complex, while in unbound docking you have to trust your sampling algorithm is efficient enough to sample them.

[monu46010]

Thank you for your response. I was confused a bit as I said earlier and now I am clear. Well, my next question is that in case of bound docking if the starting structure is the native structure, what actually we look for in bound docking, unless the interface side chains are repacked again to remove any native bias from docking calculation.

[João Rodrigues]

It's the 'easy' test. If your algorithm cannot perform satisfactorily in a bound docking scenario, it's not working.