On 04/08/2011 05:19 PM, Cale Dakwar wrote:
> Hello all,
>
> Given a PDB file of a newly solved protein structure, what is the standard
> procedure for assigning regions of secondary structure? And by this I mean
> to ask, how does one decide which residues form beta strands, which alpha
> helices, and so on? Is DSSP sufficient for this? Are we supposed to
> manually walk through the entire molecule and assign secondary structure as
> we deem appropriate based on hydrogen bonding behaviour? Some other
> procedure? And what of structures solved to ~2.7 A (or worse) where we
> can't be sure of H-bonding.
>
> Cheers,
> Cale
>
There are lots of ways, but I use PISA - it gives lots of other useful
info as well, and a nice format..
Eleanor
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