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Forgive me if this question is too trivial.

I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this?

Is there any script(python, R) so that we can download the structure from the website(like RCSB)?

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  • $\begingroup$ Welcome, parse the pdb and then run a Pymol script. Otherwise Biopython will have a fetch which will likely pull down the pdb. Be careful of the format. $\endgroup$
    – M__ ♦
    Commented Sep 16, 2019 at 16:03
  • $\begingroup$ Thanks @MichaelG. As you understand, I am very novice in this field, can you be more specific with the answer. Like any link or blog. $\endgroup$
    – Pratik Dutta
    Commented Sep 16, 2019 at 16:52
  • $\begingroup$ Hi I've a lot on right now and I don't do Ensembl (I just use Genbank) so I'm not sure how to parse Ensembl seq -> pdb codes. Emily from Ensembl is on the forum, and might help. $\endgroup$
    – M__ ♦
    Commented Sep 16, 2019 at 16:56
  • $\begingroup$ Again you have to be super careful of the pdb formatting. Finally you might want to split this into 2 questions, i.e. I think this involves 1. parsing 2. downloading. $\endgroup$
    – M__ ♦
    Commented Sep 16, 2019 at 17:05

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Ensembl to PDB

So the dataset you need is from SIFT. There is one with Ensembl IDs. Majorly this also includes what chain is your peptide and what is the offset. About the latter, I actually wrote a blog post about it recently.

PDB download

Using Python, the Biopython PDB module is very good. Although the PyMol module is more powerful. But as you want only coordinates (right?), you'd best use the former, which has a better documentation.

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