acc.dssp: Compute Residue Accessibility and SASA

In ptm: Analyses of Protein Post-Translational Modifications

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, aa = 'all')

Arguments

pdb	is either a PDB id, or the path to a pdb file.
aa	one letter code for the amino acid of interest, or 'all' for all the protein residues.

Details

You must have installed DSSP on your system and in the search path for executables.

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 (Ų), 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.

Author(s)

Juan Carlos Aledo

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

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

Examples

## Not run: acc.dssp('3cwm')

ptm documentation built on Aug. 7, 2022, 5:05 p.m.