DISULFINDER(1)

📦
version 1.2.11 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

✨ DISULFINDER ✨ (section 1, user commands, bestie)

okay so you found the disulfinder manual and honestly? good for you. this is the whole thing, nothing skipped, just with way better vibes 💅

🌸 NAME 🌸

disulfinder — cysteines disulfide bonding state and connectivity predictor

like, it predicts disulfide stuff. iconic behavior, no cap.

🎀 SYNOPSIS 🎀

disulfinder [OPTIONS]

🦋 DESCRIPTION 🦋

so disulfinder is for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from sequence alone. just the sequence. nothing else. main character energy fr fr ✨

disulfide bridges play a major role in the stabilization of the folding process for several proteins. so predicting disulfide bridges from sequence alone is therefore useful for the study of structural and functional properties of specific proteins. also, knowledge about the disulfide bonding state of cysteines may help the experimental structure determination process and may be useful in other genomic annotation tasks. multitasking queen 👑

disulfinder predicts disulfide patterns in two computational stages:

  1. the disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary classifier
  2. cysteines that are known to participate in the formation of bridges are paired by a Recursive Neural Network to obtain a connectivity pattern

two-stage pipeline. ate and left no crumbs 🍓

📚 REFERENCES 📚

A. Ceroni, A. Passerini, A. Vullo and P. Frasconi. DISULFIND: a Disulfide Bonding State and Cysteine Connectivity Prediction Server, Nucleic Acids Research, 34(Web Server issue):W177-W181, 2006.

For the disulphide connectivity predictor see:

A. Vullo and P. Frasconi. Disulfide Connectivity Prediction using Recursive Neural Networks and Evolutionary Information, Bioinformatics, 20, 653-659, 2004.

For the cystein bonding state predictor see:

P. Frasconi, A. Passerini, and A. Vullo. A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines, Proc. IEEE Workshop on Neural Networks for Signal Processing, pp.25-34, 2002. A.Ceroni, P.Frasconi, A.Passerini and A.Vullo. Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines, Journal of VLSI Signal Processing, 35, 287-295, 2003.

cite your sources bestie, it's giving academic excellence 🎓

✨ OPTIONS ✨

  • -a, --alternatives=NUMBER — alternative connectivity patterns (default=3)
  • -o, --output=DIR — output dir where predictions will be saved (default=$PWD)
  • -p, --psi2=FILE|DIR — input in psi2 format (PSI-BLAST Matrix in ASCII), either a single file or a directory(?). Generate this with "blastpgp -j <N> -Q FILE" where N >= 2.
  • -r, --rootdir=DIR — work directory (default=~/disulfinder)
  • -k, --pkgdatadir=DIR — package data directory containing Models (default=/usr/share/disulfinder)
  • -F, --format={html|ascii} — output format type (default=ascii)
  • -d --blastdb=DIR — blastpgp -d option (default=/data/sp+trembl)
  • -c, --cleanpred — cleanup intermediate prediction files (default=false)
  • -P, --usepssm — use pssm instead of counts for profiles (default=false)
  • -C, --knownbondingstate — assume bonding state is known (one file for each chain in directory <rootdir>/Predictions/Bondstate/Viterbi) (default=false)
  • -v, --version — disulfinder version
  • -?, --help — help screen
not me listing every single one of these. yes bestie, all twelve. you're welcome 💖

🌈 EXAMPLES 🌈

"disulfinder -a 1 -p
/usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb -o
./disulfinder_results_dir"

copy-paste that and you're literally a bioinformatician now 🧚

🗂️ FILES 🗂️

  • /usr/share/disulfinder — default package data directory
  • ~/disulfinder — default work directory

⚠️ RESTRICTIONS ⚠️

The work directory is not cleaned up automatically.

bestie. it does NOT clean up after itself. that's on you. go delete your own mess 🙈

👑 AUTHOR 👑

Ceroni A, Passerini A, Vullo A, Frasconi P.

Packaging by Laszlo Kajan <lkajan@rostlab.org>

GPL

🔍 SEE ALSO 🔍

See official web site for help: <http://disulfind.dsi.unifi.it/>

DISULFIND: a disulfide bonding state and cysteine connectivity prediction server: <http://www.ncbi.nlm.nih.gov/pubmed/?term=16844986[uid]>

and that's the whole page, bestie, you made it to the end 🫶 this was disulfinder version 1.2.11, dated 2022-01-20, from the User Commands manual. go predict some disulfide bridges. slay. 💅💖✨

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