Mon, Dec. 14th 2009
London
Hello,
I think you can you SSM
Secondary Structure Matching
at PDBe
http://www.ebi.ac.uk/msd-srv/ssm/
you can upload your coordinate file
and try to match to the whole of PDB.
Hope it helps
Miri
On Mon, 14 Dec 2009, Patrick Loll wrote:
> I have a 10-residue stretch of a protein that adopts an interesting conformation; I'd like
> to know if this conformation occurs in other proteins. I'd welcome suggestions for tools
> that will allow me to to search for this peptide conformation in the PDB.
> I naturally thought of DALI, but it seems to require a minimum length of 30 residues.
>
> Thanks,
>
> Pat
>
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> Patrick J. Loll, Ph. D.
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> Professor of Biochemistry & Molecular Biology
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Dr Miri Hirshberg
European Bioinformatics Institute UK
PDBe - EBI -EMBL
http://www.ebi.ac.uk/pdbe
Phone: +44 (0) 1223 492647
FAX: +44 (0) 1223 494468
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