Question: resource for structural class of proteins
0
gravatar for RT!37
4.0 years ago by
RT!3710
India
RT!3710 wrote:

Is there any resource from which structural class of proteins using their uniprot ids can be retrieved????

sequence • 901 views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by RT!3710
1
gravatar for Persistent LABS
4.0 years ago by
Pune
Persistent LABS740 wrote:

Hi

You can do it in 2step.

  1. Map uniprot IDs to PDB Ids using IDmapping tool (http://www.uniprot.org/uploadlists/)
  2. Go PDB advanced search, input pdb ids comma separated, submit, then generate custom report where u can select SCOP IDS.

Results can be downloaded as excel file.

Also you can explore : REST services of PDBe (https://www.ebi.ac.uk/pdbe/api/doc/sifts.html) and PDB (http://www.rcsb.org/pdb/software/rest.do)

Let me know if this does not help.

Thanks

Priyabrata Panigrahi

Persistent LABS

ADD COMMENTlink written 4.0 years ago by Persistent LABS740

Thanks Priyabrata !! The two step procedure is working...!!! Actually I am trying to get SCOP class using Uniprot Ids, but the downloaded excel file have SCOP Ids.

ADD REPLYlink written 4.0 years ago by RT!3710
1

You can refer to these lists to get class information using scop ids.

http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.75

http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.75

Let me know if you need help in parsing the file. Can you post sample scop ids that you obtained after mapping?

Thanks

Priyabrata

Persistent LABS

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Persistent LABS740
0
gravatar for genomax
4.0 years ago by
genomax90k
United States
genomax90k wrote:

You can search the SCOPe database. Example - P06213.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by genomax90k

Thanks genomax2 !!! Example helped me to understand that single Uniprot id can belong to more than 1 class !!!

ADD REPLYlink written 4.0 years ago by RT!3710
0
gravatar for RT!37
4.0 years ago by
RT!3710
India
RT!3710 wrote:

Thanks Priyabrata...

Sample: Id retriving Input : A0A4Z3,A0A8M2,A0AT29,A0AT32,A0AT33,A0AV96,A0AVK6,A0AVT1,A0FGR8,A0FGR9,A0FKI7 output pdbs were submitted to Advanced search and Scop Ids mapped

Only Output: 2DIS A 131532 [8-103] A0AV96

SCOp Id 131532 : when mapped with parseable file ( as provided in link by you) Results is 131532 px d.58.7.1 d2disa1 2dis A:8-103 which means 131532 belongs to Alpha and beta proteins (a+b).

Single uniprot id can harbor folds belonging to multiple Class , therefore a protein will be annotated with multiple structural class.

Please correct me if I am misinterpreting the results.

....

ADD COMMENTlink written 4.0 years ago by RT!3710
1

Yes you are right d.58.7.1 means class label is d (a+b protein).

Also you are correct that a protein can have multiple functional domains and each functional domains can be made up of multiple structural folds. SCOP classifies proteins based on fold-similarity. Thus for a single protein, there can be many SCOP domains, thus can have multiple scop ids mapped.

In order to understand better you can explore few entries PDB under Annotation section. You will see several SCOP domains can be present for a single PDB entries.

ADD REPLYlink written 4.0 years ago by Persistent LABS740

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized. SUBMIT ANSWERS should be used only for new answers to original question.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by genomax90k

Thanks Priyabrata !!

ADD REPLYlink written 4.0 years ago by RT!3710
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