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
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