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Get nucleic acids' chain names from PDB API

Bioinformatics Asked by rtviii on February 21, 2021

There is a place in my pipeline where I call PDB’s API with a ribosomal id to get all the subchains of that molecule programmatically

I’d like to separate subchains that are proteins from nucleic acids in the response, or at least know how to get the chain-ids of the nucleic acids so that i can exclude them from all manually.

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Wondering if there is some query parameter like is_nucleic_acid in the PDB’s ADL, but that’s just a hunch. I’d be happy to learn if there is a more idiomatic way to do it( from Uniprot mappings maybe? ).

My query as of now looks like when i want to get, say uniprot acccessions for subchains(in fl):

const PDBSearchSelect = "https://ww.ebi.ac.uk/pdbe/search/select?"";
const params = { 
// this is of the form "3j9m", "5afi", etc...   
q: `${input.toLowerCase()}`,        
//wondering if there is an "fl" parameter to get all nucleic acids
fl: "molecule_name, uniprot_id, uniprot_accession, struct_asym_id,...other", 
//
rows: "200"
};

axios.get(PDBSearchSelect, {params}).... => ..

I would actually be super grateful if somebody could elucidate what’s the difference between

I’ve been looking at sides of the PDB API for a few weeks now and it still seems like complete babylon in terms of naming. I realize that it grew organically over years.

Thanks a ton.

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