[Protein-analysis] Re: pdb-l: About PDB Files and Secondary
(by pcxpj1 from nottingham.ac.uk)
Wed Apr 23 15:34:07 EST 2008
>> I'm doing a project on "Protein Contact Map Prediction" and I use
>> 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 ?
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