I am not sure if this is the best way but I always use Blastp and search
against PDB. Dali search would be more appropriate if you have a structure of
your protein.
Zhen
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gloria
Borgstahl
Sent: Thursday, August 22, 2013
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Dear G,
if you only have the sequence, I suggest a BLAST search
(http://blast.ncbi.nlm.nih.gov/Blast.cgi), if you do have the
coordinates, you can use the DALI server
(http://ekhidna.biocenter.helsinki.fi/dali_server/start)
Regards,
Tim
On
Dear Gloria,
HHpred.
Best wishes,
Tomas
On Thu, Aug 22, 2013 at 4:14 PM, Gloria Borgstahl gborgst...@gmail.com wrote:
We have a protein sequence that probably contains OB folds. What is the
best way to search for the top structural homologs to this sequence in the
pdb? G
Instead of DALI, you might also want to try SALAMI
(http://www.zbh.uni-hamburg.de/salami) for your structure searches.
Tommy
On Aug 22, 2013, at 5:17 PM, Tim Gruene wrote:
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Dear G,
if you only have the sequence, I suggest a BLAST search
Dear Gloria,
If you are searching with a protein sequence, you could also try FFAS
(ffas.burnham.org/). This will perform profile-profile alignments to do fold
recognition. Works quite well for low homology cases in particular.
HTH and best wishes,
Mohammad
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We have a
...@strubi.ox.ac.uk]
Sent: Thursday, August 22, 2013 11:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] structural search for homologs in pdb?
Dear Gloria,
If you are searching with a protein sequence, you could also try FFAS
(ffas.burnham.org/). This will perform profile-profile alignments
On Thu, 22 Aug 2013, Gloria Borgstahl wrote:
We have a protein sequence that probably contains OB folds. What is the
best way to search for the top structural homologs to this sequence in the
pdb? G
Hi Gloria,
If you expect decent sequence simnilarity to one or more proteins in the PDB,
Hi Gloria,
You can paste your protein sequence directly into the text search box of the
RCSB PDB website (http://www.rcsb.org), and choose one of the sequence search
autosuggestions.
You can also to try the PSI-BAST search to find more distantly related
homologs: click on the Sequence option