Get a list of PDB id from a list of sequence protein number ?

Question

[Bioinformatics313]

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

[Ram]

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.

[Bioinformatics313]

Sorry and thanks for your notice!

[Joe]

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.

[Bioinformatics313]

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

Answer 1

[Elisabeth Gasteiger]

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 ?

[Bioinformatics313]

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.