Hi Dan,
>>>> I'm doing a project on "Protein Contact Map Prediction" and I use
>> some
>> features for nueral network's input, including Secondary Structure
>> of a
>> given Amino Acid. There are several ways:
>>>> 1- getting dssp file for each pdb file (from ftp server)
>> This method has the advantage of giving you a consistent definition of
> what is helix / sheet / turn / etc., but the disadvantage of sometimes
> missing short regions of sheet in particular.
>
Which region do you mean DSSP might miss ? The terminal ends of the
strands in a sheet, the terminal strands of the sheet or perhaps the
interrupted strands in a sheet ?
Would you please share further details, any statistics or any
reference that discusses these missing regions please ?
Many thanks,
-Pooja
