The backbone angle search in pdbemotif should limit it to particular secondary structure.
Good luck! Andy ________________________________________ From: xiaolei...@gmail.com [xiaolei...@gmail.com] Sent: October 26, 2017 5:53 PM To: Andrew Lovering; Joana Pereira Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids) Dear All, Thanks for the suggestions! I tried MPI pattern search, MOTIF2 as Andrew suggested, they worked fine to pull out of the PDB containing short sequences. What I need to do is a little bit more, I'd also like to know my hit region's secondary structure (helix, sheet, or loop), MPI and MOTIF2 usually pulls out tons of sequences, then at this stage I have to manually go to each PDB, check the hit region's secondary structure. I wonder if there is a tool to do both, i.e., let's say I could search for short sequences in only helix region or loop region of PDB files? On Thu, Oct 26, 2017 at 1:28 AM, Andrew Lovering <a.lover...@bham.ac.uk<mailto:a.lover...@bham.ac.uk>> wrote: 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<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of xiaolei...@gmail.com<mailto:xiaolei...@gmail.com> Sent: 26 October 2017 04:40 To: 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. ".
