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"
FILES¶
- /usr/share/disulfinder
- default package data directory
- ~/disulfinder
- default work directory
RESTRICTIONS¶
The work directory is not cleaned up automatically.
AUTHOR¶
Ceroni A, Passerini A, Vullo A, Frasconi P.
Packaging by Laszlo Kajan <lkajan@rostlab.org>
COPYRIGHT AND LICENSE¶
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]>
