get.area()

Description

Computes Online Surface Energies Using the Getarea Server

Usage

get.area(pdb, keepfiles = FALSE)

Arguments

pdb is either a PDB id, or the path to a pdb file.

keepfiles logical, if TRUE the dataframe will be saved in the working directory and we will keep the getarea txt file.

Value

This function returns a dataframe containing the requested information.

References

• Fraczkiewicz, R. and Braun, W. (1998) J. Comp. Chem. 19, 319-333.

Details

Analysis of protein commonly requires the partition of their structure into regions such as the surface, interior, or interface. Whenever you are interested into analysing such a partition in a particular protein, the following function of the ptm package may be of help:

• acc.dssp
• get.area (the current document)
• atom.dpx
• res.dpx
• stru.part

The function get.area() returns the surface energies computed as described by Fraczkiewicz & Braun. Further details can be obtained here.

Using as example the human hexokinase 1, which is a monomeric protein, the output of the current function would look something like this:

hHK1 <- get.area(pdb = '1cza')
kable(head(hHK1))