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 --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [email protected]
------------------------------------ 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 ------------------------------------
