rfamPDBMapping: Retrieve PDB entries with the 3D structure of members of an...

In rfaRm: An R interface to the Rfam database

Description

Retrieves entries of the PDB database with the experimentally solved 3D structure of members of the specified Rfam family, with correspondances between residues of the PDB structure and positions in the covariance model of the Rfam family. If a filename is provided, the list of PDB entries will be saved to the path specified through filename as a tab-delimited file.

Usage

rfamPDBMapping(rfamFamily, filename=NULL)

Arguments

rfamFamily	string with an Rfam family accession or ID for which the matching PDB entries should be retrieved.
filename	string indicating a path to which the retrieved PDB entries should be written as a tab-delimited file. In the default behaviour, filename=NULL, and no file will be written. Instead, the PDB entries will just be returned as a data frame.

Value

A data frame with PDB entries with experimentally solved 3D structures of members of the specified Rfam family, as well as correspondances between residues of the PDB structures and positions of the covariance model of the Rfam family. The data frame contains the following columns:

Rfam accession	Rfam accession of the Rfam family
PDB ID	ID of the PDB entry with a 3D structure of a member of the Rfam family
Chain	ID of the chain of the PDB entry that contains the coordinates for the 3D structure of a member of the Rfam family
PDB start residue	First residue of the 3D structure that can be matched to the sequence of a member of the Rfam family
PDB end residue	Last residue of the 3D structure that can be matched to the sequence of a member of the Rfam family
CM start position	First position of the covariance model of the Rfam family that can be matched to the 3D structure
CM end position	Last position of the covariance model of the Rfam family that can be matched to the 3D structure
eValue	Expectation value for the alignment of the sequence of the 3D structure to the Rfam family
Bit score	Bit score for the alignment of the sequence of the 3D structure to the Rfam family

References

Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov, Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D335–D342, https://doi.org/10.1093/nar/gkx1038

https://docs.rfam.org/en/latest/api.html

Examples

# Generate a data frame with the PDB structures of members of the Rfam family
# with ID "FMN"

rfamPDBMapping("FMN")

# Generate a data frame with the PDB structures of members of the Rfam family
# with accession "RF00174", and save the resulting PDB entries as a
# tab-delimited text file.

rfamPDBMapping("RF00174", filename="RF00174PDBentries.txt")

rfaRm documentation built on March 16, 2021, 6:01 p.m.