Dear Rex,
PDBeMotif is an opensource search tool which works with many motifs as
3D structural as sequence, it can search for ligand environment and
perform 3D search for similar cliffs in proteins.
The tool creates a relational database, it has a data loader and a
search interface.
The database can be powered by Oracle or PostgreSQL (a free RDBMS).
You could install it locally and load your private data.
The public online version for all PDB entries is available here:
http://www.ebi.ac.uk/pdbe-site/pdbemotif
It has statistics with respect of which motifs are included into a
sequence given its UniPROT id:
http://www.ebi.ac.uk/pdbe-site/pdbemotif/start?tab=motifinclstats
example for Q50EJ2 UniPROT id with respect of small 3d structural motifs
(beta-turn like) :
http://www.ebi.ac.uk/pdbe-site/pdbemotif/start?tab=motifinclstats&pattern1=Q50EJ2&against=sm3d&include=includes
example for Q50EJ2 UniPROT id with respect of PROSITE motifs:
http://www.ebi.ac.uk/pdbe-site/pdbemotif/start?tab=motifinclstats&pattern1=Q50EJ2&against=prosite&include=includes
example for Q50EJ2 UniPROT id with respect of PFAM domains:
http://www.ebi.ac.uk/pdbe-site/pdbemotif/start?tab=motifinclstats&pattern1=Q50EJ2&against=pfam&include=includes
Do not hesitate to contact me, have you any questions with this respect
Adel.
Adel Golovin
PDBe
EMBL-EBI
+44 01223 492531
golo...@ebi.ac.uk
*Does anyone know of a program designed to both store information on
functional motifs in proteins, as described in the literature, and to
retrieve such motifs within a given protein sequence?*
**
*Rex Palmer*
*Birkbeck College*
**
