[Protein-analysis] Re: pdb-l: About PDB Files and Secondary Structures

[Pooja Jain]

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