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
:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] structural search for homologs in pdb?
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
The information in this e-mail is intended only
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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,
: [ccp4bb] structural search for homologs in pdb?
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
