ProteinSecondaryStructures.jl

ProteinSecondaryStructures.jl parses STRIDE and DSSP secondary structure prediction outputs, to make them convenient to use from Julia.

Installation

In Julia, install ProteinSecondaryStructures with:

julia> import Pkg; Pkg.add("ProteinSecondaryStructures")

There is no need to independently install STRIDE or DSSP.

Related packages

• BioStructures.jl: provides secondary structure calculations in the context of a broader functionality of reading and manipulating protein structures.
• MolSimToolkit.jl: provides secondary structure calculations for molecular dynamics simulations.

References

If you use the STRIDE algorithm for secondary structure prediction, please cite:

• Frishman,D & Argos,P. (1994) Knowledge-based secondary structure assignment. Proteins: structure, function and genetics, 23, 566-579.
• Kabsch,W. & Sander,C. (1982) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22: 2577-2637.

If you use the DSSP algorithm for secondary structure prediction, please cite:

• Joosten RP, te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, Vriend A series of PDB related databases for everyday needs. Nuc. Acids Res. 2009; 39:D411-D419.
• Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1982; 22:2577-2637.