[gmx-users] Intrinsically disordered proteins

[ms]

On 18/10/10 14:26, #ZHAO LINA# wrote:
> Hi,
>
> 1. For those intrinsically disordered proteins, the sequence is known, how the simulations will be set up, I mean, the first PDB will be needed, how to get this one? (Ideally, not necessarily to be practical)
>
> 2. suppose I got a PDB, there were several models there, let's say 16, is it acceptable to just take one, say model 1?
>
> Thanks for any answering,

That's a theoretical question which has no real "true" answer, given 
that there is no "true" structure for an IDP, but only an ensemble of 
structures.

I've seen different approaches, from using ROSETTA predictions to simply 
using random coil structures, to carefully picking ensembles from 
previous experimentally-restrained simulations. Pick up your favourite 
approach in the literature, also taking into account what you want to do.

m.

-- 
Massimo Sandal, Ph.D.
http://devicerandom.org