Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)
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. ". >>> >>> >>> >>> >>> >> >>
Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)
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. ".
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> 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. ". > > > > >
Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)
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. ".
Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)
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. ".
[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. ".
