bio3d (version 2.1-3)

dssp.pdbs: Secondary Structure Analysis of Aligned PDB Structures with DSSP

Description

Secondary structure assignment of aligned PDB structures - according to the method of Kabsch and Sander (DSSP)

Usage

dssp.pdbs(pdbs)

Arguments

pdbs

a list object of class "pdbs" (obtained with pdbaln or read.fasta.pdb).

Value

• Returns a character matrix of aligned SSE assignment corresponding to each structure in the pdbs object (row wise).

Details

This is a wrapper function for easy SSE assignment of aligned PDB structures.

References

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

See Also

dssp, pdbaln

Examples

## Fetch PDB files and split to chain A only PDB files
ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
raw.files <- get.pdb(ids, path = "raw_pdbs")
files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain")

## Sequence Alignement
pdbs <- pdbaln(files)

## SSE assignment
sse <- dssp.pdbs(pdbs)