R: Secondary Structure Analysis with DSSP or STRIDE

dssp {bio3d} | R Documentation

## Secondary Structure Analysis with DSSP or STRIDE

### Description

Secondary structure assignment according to the method of Kabsch and Sander (DSSP) or the method of Frishman and Argos (STRIDE).

### Usage

    dssp(...)

    ## S3 method for class 'pdb'
    dssp(pdb, exefile = "dssp", resno=TRUE, full=FALSE, verbose=FALSE, ...)

    ## S3 method for class 'pdbs'
    dssp(pdbs, ...)

    ## S3 method for class 'xyz'
    dssp(xyz, pdb, ...)

    stride(pdb, exefile = "stride", resno=TRUE)

    ## S3 method for class 'sse'
    print(x, ...)

### Arguments

`pdb` | a structure object of class `"pdb"`, obtained from `read.pdb`.
`exefile` | file path to the ‘DSSP’ or ‘STRIDE’ program on your system (i.e. how is ‘DSSP’ or ‘STRIDE’ invoked).
`resno` | logical, if TRUE output is in terms of residue numbers rather than residue index (position in sequence).
`full` | logical, if TRUE bridge pairs and hbonds columns are parsed.
`verbose` | logical, if TRUE ‘DSSP’ warning and error messages are printed.
`pdbs` | a list object of class `"pdbs"` (obtained with `pdbaln` or `read.fasta.pdb`).
`xyz` | a trajectory object of class `"xyz"`, obtained from `read.ncdf`, `read.dcd`, `read.crd`.
`x` | an `sse` object obtained from `dssp.pdb` or `stride`.
`...` | additional arguments to and from functions.

### Details

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

### Value

Returns a list with the following components:

`helix` | ‘start’, ‘end’, ‘length’, ‘chain’ and ‘type’ of helix, where start and end are residue numbers or residue index positions depending on the value of “resno” input argument.
`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.
`acc` | a numeric vector of solvent accessibility.
`sse` | a character vector of secondary structure type per residue.
`hbonds` | a 10 or 16 column matrix containing the bridge pair records as well as backbone NH–>O and O–>NH H-bond records. (Only available for `dssp`

### Note

A system call is made to the ‘DSSP’ or ‘STRIDE’ program, which must be installed on your system and in the search path for executables. See http://thegrantlab.org/bio3d/articles/online/install_vignette/Bio3D_install.html for instructions of how to install these programs.

For the `hbonds` list component the column names can be used as a convenient means of data access, namely:
Bridge pair 1 “BP1”,
Bridge pair 2 “BP2”,
Backbone H-bond (NH–>O) “NH-O.1”,
H-bond energy of NH–>O “E1”,
Backbone H-bond (O–>NH) “O-HN.1”,
H-bond energy of O–>NH “E2”,
Backbone H-bond (NH–>O) “NH-O.2”,
H-bond energy of NH–>O “E3”,
Backbone H-bond (O–>NH) “O-HN.2”,
H-bond energy of O–>NH “E4”.

If ‘resno=TRUE’ the following additional columns are included:
Chain ID of resno “BP1”: “ChainBP1”,
Chain ID of resno “BP2”: “ChainBP2”,
Chain ID of resno “O-HN.1”: “Chain1”,
Chain ID of resno “NH-O.2”: “Chain2”,
Chain ID of resno “O-HN.1”: “Chain3”,
Chain ID of resno “NH-O.2”: “Chain4”.

### Author(s)

Barry Grant, Lars Skjaerven (dssp.pdbs)

### 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:
https://swift.cmbi.umcn.nl/gv/dssp/.

‘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://webclu.bio.wzw.tum.de/stride/, or copy it from an installation of VMD.

### See Also

`read.pdb`, `torsion.pdb`, `torsion.xyz`, `plot.bio3d`,

`read.ncdf`, `read.dcd`, `read.prmtop`, `read.crd`,

### Examples

    ## Not run:
    ##- PDB example
    # Read a PDB file
    pdb <- read.pdb("1bg2")
    sse <- dssp(pdb)
    sse2 <- stride(pdb)

    ## Short summary
    sse
    sse2

    # Helix data
    sse$helix

    # Precent SSE content
    sum(sse$helix$length)/sum(pdb$calpha) * 100
    sum(sse$sheet$length)/sum(pdb$calpha) * 100

    ##- PDBs example
    aln  <- read.fasta( system.file("examples/kif1a.fa",package="bio3d") )
    pdbs <- read.fasta.pdb( aln )

    ## Aligned PDB defined secondary structure
    pdbs$sse

    ## Aligned DSSP defined secondary structure
    sse <- dssp(pdbs)

    ##- XYZ Trajectory
    pdb <- read.pdb("2mda", multi=TRUE)
    dssp.xyz(pdb$xyz, pdb)

    ## Note. for large MD trajectories you may want to skip some frames, e.g.
    xyz <- rbind(pdb$xyz, pdb$xyz)       ## dummy trajectory
    frames <- seq(1, to=nrow(xyz), by=4) ## frame numbers to examine
    ss <- dssp.xyz(xyz[frames, ], pdb)      ## matrix of sse frame x residue

    ## End(Not run)

[Package bio3d version 2.4-2 Index]