ptm (version 0.2.2)

acc.dssp: Compute Residue Accessibility and SASA

Description

Computes the accessibility as well as the SASA for each reside from the indicated protein.

Usage

acc.dssp(pdb, dssp = 'compute', aa = 'all')

Arguments

pdb

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

dssp

string indicating the preferred method to obtain the dssp file. It must be either 'compute' or 'mkdssp'.

aa

one letter code for the amino acid of interest, or 'all' for all the protein residues.

Value

A dataframe where each row is an individual residue of the selected protein. The variables computed, among others, are: (i) the secondary structure (ss) element to which the residue belongs, (ii) the solvent accessible surface area (sasa) of each residue in square angstrom (<U+00C5><U+00B2>), and (iii) the accessibility (acc) computed as the percent of the sasa that the residue X would have in the tripeptide GXG with the polypeptide skeleton in an extended conformation and the side chain in the conformation most frequently observed in proteins.

Details

For the given PDB the function obtains its corresponding DSSP file using the chosen method. The argument dssp allows two alternative methods: 'compute' (it calls to the function compute.dssp(), which in turn uses an API to run DSSP at the CMBI); 'mkdssp' (if you have installed DSSP on your system and in the search path for executables).

References

Miller et al (1987) J. Mol. Biol. 196: 641-656 (PMID: 3681970).

Touw et al (2015) Nucl. Ac. Res. 43(Database issue): D364-D368 (PMID: 25352545).

See Also

compute.dssp(), atom.dpx(), res.dpx(), str.part()

Examples

# NOT RUN {
acc.dssp('3cwm')
acc.dssp(pdb = '3cwm', aa = 'M')
# }