find.pdbs: Find PDB structures for a Uniprot accession
In jweile/mavevis: Visualization for MaveDB

find.pdbs

R Documentation

Find PDB structures for a Uniprot accession

Description

Finds PDB structures that contain the protein indicated by the given Uniprot accession. Checks for a local cache file of previous results. If such a cache exists, the pre-calculated results will be returned, otherwise queries to Uniprot and PDB will be made.

Usage

find.pdbs(acc, filterRange = NA)

Arguments

acc

the Uniprot accession

Value

a data.frame with the following columns:

pdb: the PDB accession of the structure
method: the experimental method for this structure, e.g NMR, X-ray or Model
resolution: the resolution of this structure, in Angstrom.
mainChains: a /-separated list of chain IDs that correspond to the protein with the given Uniprot accession.
start: the first amino acid of the protein represented in the structure
end: the last amino acid of the protein represented in the structure
partners: a comma-separated list of interaction partners if the structure is of a complex. Each item follows the syntax chainID=UniprotID/ProteinName