Question: Get a list of PDB id from a list of sequence protein number ?
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gravatar for Bioinformatics313
22 months ago by
USA,CO
Bioinformatics3130 wrote:

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

tool protein pdb gene • 1.0k views
ADD COMMENTlink modified 22 months ago by Elisabeth Gasteiger1.7k • written 22 months ago by Bioinformatics3130

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 written 22 months ago by RamRS27k

Sorry and thanks for your notice!

ADD REPLYlink written 22 months ago by Bioinformatics3130

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 written 22 months ago by Joe17k

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

ADD REPLYlink written 22 months ago by Bioinformatics3130
0
gravatar for Elisabeth Gasteiger
22 months ago by
Geneva
Elisabeth Gasteiger1.7k wrote:

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 modified 22 months ago • written 22 months ago by Elisabeth Gasteiger1.7k

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 written 22 months ago by Bioinformatics3130
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