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

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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.

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Sorry and thanks for your notice!

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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.

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

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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 ?