dssp {bio3d}R Documentation

Secondary Structure Analysis with DSSP

Description

Secondary structure assignment according to the method of Kabsch and Sander.

Usage

dssp(pdb, exepath = "", resno=TRUE)

Arguments

pdb a structure object of class "pdb", obtained from read.pdb.
exepath path to the ‘DSSP’ program on your system (i.e. the directory where ‘DSSP’ is stored).
resno logical, if TRUE output is in terms of residue numbers rather than residue index (position in sequence).

Details

This function calls the ‘DSSP’ program to define secondary structure and psi and phi torsion angles.

Value

Returns a list with the following components:

helix ‘start’, ‘end’ and ‘length’ of H type sse, where start and end are residue numbers “resno”.
sheet ‘start’, ‘end’ and ‘length’ of E type sse, where start and end are residue numbers “resno”.
turn ‘start’, ‘end’ and ‘length’ of T type sse, where start and end are residue numbers “resno”.
phi a numeric vector of phi angles.
psi a numeric vector of psi angles.

Note

A system call is made to the ‘DSSP’ program, which must be installed on your system and in the search path for executables.

Author(s)

Barry Grant

References

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

‘DSSP’ is the work of Kabsch and Sander: Kabsch and Sander (1983) Biopolymers. 12, 2577–2637.

For information on obtaining ‘DSSP’, see:
http://swift.cmbi.ru.nl/gv/dssp/.

See Also

read.pdb, stride, torsion.pdb, torsion.xyz

Examples

## Not run: 
# Read a PDB file
pdb <- read.pdb(system.file("examples/d1bg2__.ent", package="bio3d"))
sse <- dssp(pdb)

# Helix data
sse$helix

# Precent SSE content
sum(sse$helix$length)/sum(pdb$calpha) * 100
sum(sse$sheet$length)/sum(pdb$calpha) * 100
## End(Not run)

[Package bio3d version 1.0-5 Index]