DISULFINDER(1)							   User Commands						    DISULFINDER(1)

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]>

1.2.11								    2012-04-07							    DISULFINDER(1)