EnglishFrenchSpanish

Ad


OnWorks favicon

disulfinder - Online in the Cloud

Run disulfinder in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command disulfinder that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


disulfinder - cysteines disulfide bonding state and connectivity predictor

SYNOPSIS


disulfinder [OPTIONS]

DESCRIPTION


'disulfinder' is for predicting the disulfide bonding state of cysteines and their
disulfide connectivity starting from sequence alone. Disulfide bridges play a major role
in the stabilization of the folding process for several proteins. Prediction of disulfide
bridges from sequence alone is therefore useful for the study of structural and functional
properties of specific proteins. In addition, knowledge about the disulfide bonding state
of cysteines may help the experimental structure determination process and may be useful
in other genomic annotation tasks. '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.

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.

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

EXAMPLES


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

Use disulfinder online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    AstrOrzPlayer
    AstrOrzPlayer
    AstrOrz Player is a free media player
    software, part based on WMP and VLC. The
    player is in a minimalist style, with
    more than ten theme colors, and can also
    b...
    Download AstrOrzPlayer
  • 2
    movistartv
    movistartv
    Kodi Movistar+ TV es un ADDON para XBMC/
    Kodi que permite disponer de un
    decodificador de los servicios IPTV de
    Movistar integrado en uno de los
    mediacenters ma...
    Download movistartv
  • 3
    Code::Blocks
    Code::Blocks
    Code::Blocks is a free, open-source,
    cross-platform C, C++ and Fortran IDE
    built to meet the most demanding needs
    of its users. It is designed to be very
    extens...
    Download Code::Blocks
  • 4
    Amidst
    Amidst
    Amidst or Advanced Minecraft Interface
    and Data/Structure Tracking is a tool to
    display an overview of a Minecraft
    world, without actually creating it. It
    can ...
    Download Amidst
  • 5
    MSYS2
    MSYS2
    MSYS2 is a collection of tools and
    libraries providing you with an
    easy-to-use environment for building,
    installing and running native Windows
    software. It con...
    Download MSYS2
  • 6
    libjpeg-turbo
    libjpeg-turbo
    libjpeg-turbo is a JPEG image codec
    that uses SIMD instructions (MMX, SSE2,
    NEON, AltiVec) to accelerate baseline
    JPEG compression and decompression on
    x86, x8...
    Download libjpeg-turbo
  • More »

Linux commands

  • 1
    abi-tracker
    abi-tracker
    abi-tracker - visualize ABI changes
    timeline of a C/C++ software library.
    DESCRIPTION: NAME: ABI Tracker
    (abi-tracker) Visualize ABI changes
    timeline of a C/C+...
    Run abi-tracker
  • 2
    abicheck
    abicheck
    abicheck - check application binaries
    for calls to private or evolving symbols
    in libraries and for static linking of
    some system libraries. ...
    Run abicheck
  • 3
    couriermlm
    couriermlm
    couriermlm - The Courier mailing list
    manager ...
    Run couriermlm
  • 4
    couriertcpd
    couriertcpd
    couriertcpd - the Courier mail server
    TCP server daemon ...
    Run couriertcpd
  • 5
    gbklatex
    gbklatex
    bg5latex - Use LaTeX directly on a Big5
    encodedtex file bg5pdflatex - Use
    pdfLaTeX directly on a Big5 encodedtex
    file bg5+latex - Use LaTeX directly on a
    Big5+...
    Run gbklatex
  • 6
    gbkpdflatex
    gbkpdflatex
    bg5latex - Use LaTeX directly on a Big5
    encodedtex file bg5pdflatex - Use
    pdfLaTeX directly on a Big5 encodedtex
    file bg5+latex - Use LaTeX directly on a
    Big5+...
    Run gbkpdflatex
  • More »

Ad