I would guess that you want to search PDB for a small motif you've observed in a structure of yours, looking to find examples of it used in same context? If that's true, I would recommend PDBemotif, put the sequence in, and then use the backbone psi phi angles of your motif as a secondary constraint in the search, increasing/decreasing the angle tolerance as appropriate. If I’m incorrect, and you just want to find examples of a short motif, this webserver is awesome – you can also limit it by taxonomy: http://www.genome.jp/tools/motif/MOTIF2.html
Best Andy From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xiaolei...@gmail.com Sent: 26 October 2017 04:40 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] blast pdb for a very short sequence (3 amino acids) Dear CCP4BB members, Sorry this post is off-topic. I am asking is there a way to blast pdb for a very short sequence like 2 or 3 amino acids? I tried this for a positive control in pdb database but returned that "Your search parameters were adjusted to search for a short input sequence." and "No significant similarity found. ".
