Biostar Beta. Not for public use.
Get a list of PDB id from a list of sequence protein number ?
0
Entering edit mode
2.1 years ago
USA,CO

Hey guys , I hope you are doing well. I am working on a project of phosphorylation ,and I am creating a database of some proteins. I have a list of protein accession ids ,and I need to get the corresponding PDB code for each one . I want to get them by the code of python or biopython tools. Please , any suggestion will really be appreciated . Thanks

ADD COMMENTlink
0
Entering edit mode

Please edit this post and change it to a Question. A Tool type post should only be used when a new tool is being introduced to the community.

ADD REPLYlink
0
Entering edit mode

Sorry and thanks for your notice!

ADD REPLYlink
0
Entering edit mode

You’ll likely want to use some or all of the NCBI eutils and PDBs RESTful API. I don’t have a concrete answer for you at the moment, but that should give you somewhere to start.

ADD REPLYlink
0
Entering edit mode

Thanks bro, I am working with it by the code ,and I do not retrieve the data manually . I appreciate your reply.

ADD REPLYlink
0
Entering edit mode
18 months ago
Geneva

If your protein identifiers are from UniProtKB, you can use the UniProt IDmapping or Batch retrieve service at https://www.uniprot.org/uploadlists. You can either map from UniProtKB to PDB, or from UniProtKB to UniProtKB and then customize your results by adding a column for PDB cross-references and removing any unwanted ones. Results can be downloaded in various formats, and the service can also be used programmatically: https://www.uniprot.org/help/api

If you have any additional questions about UniProt, please don't hesitate to contact the UniProt helpdesk. See also this thread: How to get PDB ID from sequence accession number ?

ADD COMMENTlink
0
Entering edit mode

Thanks man, I really appreciate your answer. Actually , I was using this website to get PDB code by uploading protein ids file as csv file, however, I would like to retrieve PDB code by python or Bio-python code. I am currently working on the code and I will done with it soon! Thanks again for your reply.

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1