From 67961931e67e2d105404a3166b4f13e5145987ef Mon Sep 17 00:00:00 2001 From: anton083 Date: Thu, 26 Oct 2023 01:11:44 +0200 Subject: [PATCH] Update README.md --- README.md | 35 +++++++++++++++++++++++++++++++++-- 1 file changed, 33 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ab60dc0..1d929c0 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,35 @@ # AssigningSecondaryStructure -[![Build Status](https://github.com/anton083/AssigningSecondaryStructure.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/anton083/AssigningSecondaryStructure.jl/actions/workflows/CI.yml?query=branch%3Amain) -[![Coverage](https://codecov.io/gh/anton083/AssigningSecondaryStructure.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/anton083/AssigningSecondaryStructure.jl) +[![Build Status](https://github.com/MurrellGroup/AssigningSecondaryStructure.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/MurrellGroup/AssigningSecondaryStructure.jl/actions/workflows/CI.yml?query=branch%3Amain) +[![Coverage](https://codecov.io/gh/MurrellGroup/AssigningSecondaryStructure.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/MurrellGroup/AssigningSecondaryStructure.jl) + +This package provides a simple way to assign secondary structure to a protein sequence. It is based on the [DSSP](https://swift.cmbi.umcn.nl/gv/dssp/) algorithm. It was ported from the [PyDSSP](https://github.com/ShintaroMinami/PyDSSP) package. + +```julia +julia> sscodes(dssp("1ZAK.pdb")) +"----EEEEEE-----HHHHHHHHHHHH--EE--HHHHHHHHHHH--HHHHHHHHHHH------HHHHHHHHHHHHH-HHHHH--EEEE-----HHHHHHHH-------EEEEEE--HHHHHHHH--EEEE-----EEE---------HHHHHEE------HHHHHHHHHHHHHHHHHHHH-----EEEEE----HHHHHHHHHHHHHHHHHHHHHHH-------EEEEEE-----HHHHHHHHHHHH--EE--HHHHHHHHHHH--HHHHHHHHHHH------HHHHHHHHHHHHH-HHHHH--EEEE-----HHHHHHHH-------EEEEEE--HHHHHHHH--EEEE-----EEE---------HHHHHEE------HHHHHHHHHHHHHHHHHHHH-----EEEEE----HHHHHHHHHHHHHHHHHHHHHHH---" + +``` + + +## Differences from the original DSSP +This implementation was simplified from the original DSSP algorithm: +- The implementation omits β-bulge annotation, so β-bulge is determined as a loop instead of β-strand. +- Parameters for adding hydrogen atoms are slightly different from the original DSSP, which may cause small differences in hydrogen bond annotation. +- Only supports C3 ('-', 'H', and 'E') type assignment instead of C8 type (B, E, G, H, I, S, T, and ' '). + +In spite of these simplifications, 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. + +## Reference +``` bibtex +@article{kabsch1983dictionary, + title={Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features}, + author={Kabsch, Wolfgang and Sander, Christian}, + journal={Biopolymers: Original Research on Biomolecules}, + volume={22}, + number={12}, + pages={2577--2637}, + year={1983}, + publisher={Wiley Online Library} +} +``` \ No newline at end of file