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> 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] *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. ". > > > > >
