Explanation

Overview

This package uses STRIDE or DSSP to compute secondary structures of proteins from their atomic coordinates.

The functions are divided into two groups:

  • Computing the secondary structure from a single PDB file.

  • Computing the secondary structure throughout a Molecular Dynamics Simulation.

Additionally, the subset of the strucuture that will be considered for the calculations can be defined through the interface with the PDBTools package.

Note

By default, only atoms of standard protein residues will be considered from the PDB file. It is possible to select different subsets of atoms with the selection keyword, but then STRIDE or DSSP may fail with internal errors if the residue or atom types are not recognized. The selection keyword follows the PDBTools.jl selection syntax.

Secondary structure classes

The output of STRIDE or DSSP follow the convention of secondary strucure codes, which are:

Secondary structuress codecode number
"310 helix""G"1
"alpha helix""H"2
"pi helix""I"3
"kappa helix""P"4
"turn""T"5
"beta strand""E"6
"beta bridge""B"7
"bend""S"8
"coil""C"9
"loop"" "10

See the DSSP secondary structure classification for further information.

The code number are used here to output the matrices of secondary structures obtained from trajectory runs.

Data structure

The output of the secondary structure calculations is a vector of SSData elements, with the following data, for each residue:

  • resname::String - residue name
  • chain::String - chain identifier
  • resnum::Int - residue number
  • sscode::String - secondary structure code
  • phi::Float64 - phi dihedral angle
  • psi::Float64 - psi dihedral angle
  • area::Float64 - solvent accessible area (stride specific)
  • kappa::Float64 - virtual bond angle (dssp specific)
  • alpha::Float64 - virtual torsion angle (dssp specific)

The output of stride_run or dssp_run is a vector of SSData structures, one for each residue. For example:

julia> using ProteinSecondaryStructures

# Replace the next assignment with a custom PDB file name
julia> pdbfile = ProteinSecondaryStructures.Testing.examples[1].filename
"/home/user/.julia/dev/ProteinSecondaryStructures/test/data/pdb/pdb1fmc.pdb"

julia> ss = stride_run(pdbfile);

julia> ss[1]
SSData("MET", "A", 1, "C", 360.0, 150.62, 234.4, 0.0, 0.0)

julia> ss[1].sscode
"C"

julia> class(ss[1].sscode)
"coil"