gene name to PDB ID - which database to download

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4.8 years ago

theoharis ▴ 40

Which RCSB database/s to download to enable search for PDB ID using UniProt gene name?

gene PDB 3D protein structure • 1.4k views

ADD COMMENT • link 4.8 years ago by theoharis ▴ 40

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What have you tried? The README at the ID mapping entity on UniProt Downloads mentions that it maps UniProtKB IDs to PDB IDs.

ADD REPLY • link 4.8 years ago by Ram 43k

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I am aware of this - what I was looking for is a database at _RCSB_ that contains within its PDB record the gene name that the protein is encoded by. I am presently using a POST via PHP and curl to send a XML query with a gene name from which I obtain the 4-character PDB that it is matched to. I then use this to make another query via the NGL viewer to obtain the PBD structure. I would prefer to download the entire database but don't know which is the most appropriate one.

ADD REPLY • link 4.8 years ago by theoharis ▴ 40

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