Making massive "structural querys" to PDB

Helge Weissig helgew at SDSC.EDU
Tue Sep 21 11:31:11 EST 1999


Dear Gerard,

	Prosite pattern searches are possible via
http://www.rcsb.org/pdb/cgi/queryForm.cgi . You will need to add the
"Short Sequence Pattern" query option by checking the appropriate check
box on the bottom of the form and selecting the "New Form" button.

best regards,
h.

+--------------------------------------------+
| Helge Weissig, PhD                         |
| Project Manager, Structural Bioinformatics |
| San Diego Supercomputer Center  +-----------------------------------+
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On Tue, 14 Sep 1999, Gerard Pujadas wrote:

> 
> 	Dear all,
> 
> 	I would like to know if there is any software that can do
> "structural querys" to the full PDB (or in a big PDB sample). Examples of
> such "structural querys" may be:
> 
> 	1) Search for all existing helix caps of the type "capping box"
> where the residues in N4 is Phe or Tyr, the ones in Ncap are Thr or Asp and
> the one in N3 is always Glu.
> 
> 	2) Search for a particular motif sequence in PROSITE syntax and
> report all structures where this sequence is located in a defined secondary
> structure/s.
> 
> 	These are of course examples. The "ideal" soft that I'm searching
> for need to be as flexible as possible to make all the type of "structural
> querys" you want to the PDB.
> 
> 	Many thanks in advances !!!!
> 
> 	Yours sincerely.
> 
> 	Gerard.
> 
> ===========================================================================
> DR. GERARD PUJADAS
> BIOTECNOLOGIA COMPUTACIONAL
> DEPT. BIOQUIMICA I BIOTECNOLOGIA	   E-MAIL: pujadas at quimica.urv.es
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> 
> 
> 
> 
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