Re: [ccp4bb] structural search for homologs in pdb?
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 11:15 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 for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [ccp4bb] structural search for homologs in pdb?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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 08/22/2013 05:14 PM, 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 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSFiufUxlJ7aRr7hoRAiCLAKCHDkluz9I/hs437VP1eATh+OWJYwCeIwT3 xDwgPgkom1ipFiHpBaVYhxg= =bB6q -END PGP SIGNATURE-
Re: [ccp4bb] structural search for homologs in pdb?
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
Re: [ccp4bb] structural search for homologs in pdb?
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: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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 08/22/2013 05:14 PM, 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 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSFiufUxlJ7aRr7hoRAiCLAKCHDkluz9I/hs437VP1eATh+OWJYwCeIwT3 xDwgPgkom1ipFiHpBaVYhxg= =bB6q -END PGP SIGNATURE-
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 to do fold recognition. Works quite well for low homology cases in particular. HTH and best wishes, Mohammad ---BeginMessage--- 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 ---End Message---
Re: [ccp4bb] structural search for homologs in pdb?
Hi Gloria, I've gotten useful results from these two threading / prediction servers: Raptorx and Phyre (for low homology, I found the original version works better than phyre2). Phoebe ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of moham...@strubi.ox.ac.uk [moham...@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 to do fold recognition. Works quite well for low homology cases in particular. HTH and best wishes, Mohammad
Re: [ccp4bb] structural search for homologs in pdb?
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, and if you don't have the structure of your protein, a simple FASTA search should give you the list of hits and alignments quickly. I would do that using the PDBeXplore FASTA archive browser - http://pdbe.org/fasta Simply provide your sequence (or UniProt accession) and submit. If there are hits, they will be presented in a way that allows for rapid further exploration, e.g. in terms of their CATH classifications, bound ligands or Pfam families. You can also sort the hits by E-value or %-age identity (amongst many other things) and get the alignments with your sequence in the results page. If you want to explore the interface, try http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/?seq=SVRKFTEKHEWVTTENGVGTVGISNFAQEALGDVVYCSLPEVGTKLNKQEEFGALESVKAASELYSPLSGEVTEINKALAENPGLVNKSCYEDGWLIKMTFSNPSELDELMSEEAYEKYIKSIEEtab=PDB%20entries (this uses the sequence of PDB entry 3KLR which also has an OB fold, CATH class 2.40.50). There are a number of PDBeXplore modules available (http://pdbe.org/explore), including a CATH-based browser (if you should like to analyse all the structures that contain an OB fold according to CATH). If you should have a structure, you can use PDBeFold (SSM; http://pdbe.org/fold) to quickly find and compare similar structures without taking sequence into consideration. --Gerard
Re: [ccp4bb] structural search for homologs in 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 in the top search bar and then choose options. On the advanced search page choose PSI-BLAST as the search tool. Peter Rose RCSB PDB From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gloria Borgstahl Sent: Thursday, August 22, 2013 8:15 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
