With the vast number of sequences available I doubt you’ll get any meaningful results with only 3 amino acids… However, I believe the full list of sequences in the PDB is available here for download: ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt
Using this you could run your own local scripts to do customised searches. Cheers Mike From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Xiao Lei <xiaolei...@gmail.com<mailto:xiaolei...@gmail.com>> Reply-To: Xiao Lei <xiaolei...@gmail.com<mailto:xiaolei...@gmail.com>> Date: Thursday, 26 October 2017 at 14:40 To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" <CCP4BB@JISCMAIL.AC.UK<mailto: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. ".
