Question

pdb id converter to gene id of EBI

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10.2 years ago

gbahramali ▴ 20

Hello

I have many (1000000 pdbid) pdbid, could you please tell me how convert pdb id to gene accession number.

gene • 4.3k views

ADD COMMENT • link updated 17 months ago by Ram 44k • written 10.2 years ago by gbahramali ▴ 20

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There are currently 103 199 structures in the PDB, so I don't think you have 1000 000 IDs :)
Search this site for "biomart".

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by Neilfws 49k

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OHH EXCUSE ME

YOU ARE RIGHT, I have 10000 dssp id with chain and I think that I have 5000 pdb id

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by gbahramali ▴ 20

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Does all the PDB IDs belong to human/mouse proteins? or other molecules?

ADD REPLY • link 10.2 years ago by roy.granit ▴ 890

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I think that all ,

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by gbahramali ▴ 20

Ram · Answer 1 · 2014-09-16

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10.2 years ago

cdsouthan ★ 1.9k

Conceptualy http://www.ebi.ac.uk/pdbe/ has done the mappings for you via UniProt. Quite what the most technically efficient way to mine out what you need I'll leave others to suggest. But note this lands you in the classic protein-to-gene issue that gets difficult for deep phylogeny

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by cdsouthan ★ 1.9k