Dear All, Thanks. I tried PDBemotif, indeed, it works very well!
On Thu, Oct 26, 2017 at 10:04 AM, Andrew Lovering < andrewleelover...@googlemail.com> wrote: > The backbone psi phi angle option in pdbemotif should limit hits to a > particular secondary structure. > > Good luck! > Andy > > On 26 Oct 2017 5:54 pm, "xiaolei...@gmail.com" <xiaolei...@gmail.com> > wrote: > >> 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. ". >>> >>> >>> >>> >>> >> >>
