The backbone angle search in pdbemotif should limit it to particular secondary structure.
Good luck!
Andy
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From: [log in to unmask] [[log in to unmask]]
Sent: October 26, 2017 5:53 PM
To: Andrew Lovering; Joana Pereira
Cc: [log in to unmask]
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 <[log in to unmask]<mailto:[log in to unmask]>> 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:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of [log in to unmask]<mailto:[log in to unmask]>
Sent: 26 October 2017 04:40
To: [log in to unmask]<mailto:[log in to unmask]>
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. ".
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