stride {bio3d}R Documentation

Secondary Structure Analysis with STRIDE

Description

Secondary structure assignment according to the method of Frishman and Argos.

Usage

stride(pdb, exepath = "")

Arguments

pdb a structure object of class '"pdb"', obtained from read.pdb.
exepath path to the ‘STRIDE’ program on your system (i.e. the directory where ‘STRIDE’ is stored).

Details

This function calls the ‘STRIDE’ 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 ‘STRIDE’ 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.

‘STRIDE’ is the work of Frishman and Argos: Frishman and Argos (1995) Proteins. 3, 566–579.

For information on obtaining the ‘STRIDE’ program, see:
http://www.embl-heidelberg.de/stride/stride_info.html, or copy it from an installation of VMD.

See Also

read.pdb, dssp, torsion.pdb, torsion.xyz

Examples

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