Making massive "structural querys" to PDB

Gerard Pujadas pujadas at argo.urv.es
Tue Sep 14 10:39:21 EST 1999


	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
UNIV. ROVIRA I VIRGILI                     PHONE: 34-977 559565
PLAÇA IMPERIAL TARRACO 1                   FAX: 34-977 559597
43005 TARRAGONA (CATALONIA)
STATE: SPAIN (EUROPEAN UNION)
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