Hi Sean, You could try a "scan prosite" search and tell it only to search the pdb
http://www.expasy.org/tools/scanprosite/ You would enter a search pattern such as D-A-V-E and it allows you to look for exact matches. You can also specify to look for homologues, like [DE]-A-[VLI]-[DE] This would at least give you a list of PDBs that contained your motif. HTH Dave On 05/04/2008, Sean Johnson <[EMAIL PROTECTED]> wrote: > Is there a way to search the PDB for both sequence and secondary structure > characteristics? I am trying to identify examples of a short (4 aa) > sequence located in loop or other non-helical/sheet regions. > > Thanks, > Sean Johnson > > -- > Sean Johnson, PhD > R. Gaurth Hansen Assistant Professor > Utah State University > Department of Chemistry and Biochemistry > 0300 Old Main Hill > Logan, UT 84322-0300 > (435) 797-2089 > (435) 797-3390 (fax) > [EMAIL PROTECTED] > -- ============================ David C. Briggs PhD Father & Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile ============================
