Pattern Discovery in PDB Structures of Metalloproteins

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Description

Looks for amino acid and/or nucleotide patterns coordinated to a given prosthetic centre. It also accounts for small molecule ligands. Files have to be in the local file system and contain the '.pdb' extension.

Usage

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PdPDB(path, metal, n)

Arguments

path

A string containing the path to the PDB directory

metal

A string containing the PDB chemical symbol of the target prosthetic centre; e.g. SF4 for [4Fe-4S] cluster, ZN for zinc. The PDB chemical symbol is case sensitive for macOS.

n

A numerical value that contains the number or residue in +/- n position from the ligated amino acid or nucleotide; if n=1 PdPDB searches for x(L)x motif-like chains, if n=2 for xx(L)xx. (L)igand.

Author(s)

Luca Belmonte, Sheref S. Mansy

References

Belmonte L, Mansy SS PdPDB: An R tool for pattern discovery in PDB structures of metalloproteins, (in preparation)

Examples

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################ Defining path to PDBs
path_to_PDB="inst/extdata/PDB" # this is where pdb files are

################ Research Parameters
metal="mg"  	# searches for magnesium coordinated patterns;
n=1         	# searches for x(L)x motif like patterns, (L) coordinates to MG

################ Launch PdPDB
PdPDB(path_to_PDB,metal,n)

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