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:
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))
| eleno | elety | resid | resno | areaenergy |
|---|---|---|---|---|
| 1 | N | D | 16 | 35.61 |
| 2 | CA | D | 16 | 6.26 |
| 3 | C | D | 16 | 0.00 |
| 4 | O | D | 16 | 0.00 |
| 5 | CB | D | 16 | 17.58 |
| 6 | CG | D | 16 | 1.75 |
