diff --git a/README.md b/README.md index 761b06d..8d0dc50 100644 --- a/README.md +++ b/README.md @@ -5,11 +5,13 @@ This package provides a to calculate the secondary structure using the [DSSP](https://swift.cmbi.umcn.nl/gv/dssp/) algorithm. The package was ported from the [PyDSSP](https://github.com/ShintaroMinami/PyDSSP) package. -It is not a complete implementation of DSSP, as it only assigns '-' for loops, 'H' for alpha helices, and 'E' for beta strands. - -In spite of these differences, the C3 type annotation still matches the original DSSP to a large extent. For the full DSSP algorithm, check out [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl) or [ProteinSecondaryStructures.jl](https://github.com/m3g/ProteinSecondaryStructures.jl), which both use the auto-generated [DSSP_jll.jl](https://docs.juliahub.com/General/DSSP_jll/stable/) binary. +It is not a complete implementation of DSSP, as it only assigns '-' for loops, 'H' for alpha helices, and 'E' for beta strands. In spite of that, it matches the original DSSP to a large extent, with the added advantage of being more than 10x faster. For the full DSSP algorithm, check out [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl) or [ProteinSecondaryStructures.jl](https://github.com/m3g/ProteinSecondaryStructures.jl), which both use the [DSSP_jll.jl](https://docs.juliahub.com/General/DSSP_jll/stable/) package, auto-generated using [BinaryBuilder.jl](https://github.com/JuliaPackaging/BinaryBuilder.jl). ```julia julia> join(sscodes(dssp("1ASS.pdb"))) -"---EEE-----------EEE-EEEEEE---E---HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH-----EEEE---E-HHHHHHHHHH--EEE----HHHHHHHHHHH----E-----------EEE-EEEEEEE--EEEEEEE-----------" -``` \ No newline at end of file +1-element Vector{String}: + "---EEE-----------EEE-EEEEEE---E" ⋯ 90 bytes ⋯ "--------EEE-EEEEEEE--EEEEEEE---" +``` + +## References +- [Kabsch W, Sander C (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22 (12): 2577–2637.](https://doi.org/10.1002/bip.360221211)