bio3d (version 2.1-2)

binding.site: Binding Site Residues

Description

Determines the interacting residues between two PDB entities.

Usage

binding.site(a, b=NULL, a.inds=NULL, b.inds=NULL, cut=5, hydrogens=TRUE)

Arguments

a

an object of class pdb as obtained from function read.pdb.

b

an object of class pdb as obtained from function read.pdb.

a.inds

atom and xyz coordinate indices obtained from atom.select that selects the elements of a upon which the calculation should be based.

b.inds

atom and xyz coordinate indices obtained from atom.select that selects the elements of b upon which the calculation should be based.

cut

distance cutoff

hydrogens

logical, if FALSE hydrogen atoms are omitted from the calculation.

Value

• Returns a list with the following components:
• atom.inds
  atom indices of a.
• xyz.inds
  xyz indices of a.
• resnames
  a character vector of interacting residues.
• resno
  a numeric vector of interacting residues numbers.

Details

This function reports the residues of a closer than a cutoff to b. This is a wrapper function calling the underlying function dm.xyz.

If b=NULL then b.inds should be elements of a upon which the calculation is based (typically chain A and B of the same PDB file).

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

read.pdb, atom.select, dm

Examples

pdb <- read.pdb('3dnd')

     # Binding site residues
     rec.inds <- atom.select(pdb, string='//A/1:350////')
     lig.inds <- atom.select(pdb, string='//A/351////')
     bs <- binding.site(pdb, a.inds=rec.inds, b.inds=lig.inds)

     # Interaction between peptide and protein
     rec.inds <- atom.select(pdb, string='//A/1:350////')
     lig.inds <- atom.select(pdb, string='//I/5:24////')
     bs <- binding.site(pdb, a.inds=rec.inds, b.inds=lig.inds)

     # Interaction between two PDB entities
#     rec <- read.pdb("receptor.pdb")
#     lig <- read.pdb("ligand.pdb")
     rec <- trim.pdb(pdb, inds=rec.inds)
     lig <- trim.pdb(pdb, inds=lig.inds)
     bs <- binding.site(rec, lig, hydrogens=FALSE)