disulfinder - cysteines disulfide bonding state and connectivity
predictor
'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.
- 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.
- -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
"disulfinder -a 1 -p
/usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb -o
./disulfinder_results_dir"
- /usr/share/disulfinder
- default package data directory
- ~/disulfinder
- default work directory
The work directory is not cleaned up automatically.
Ceroni A, Passerini A, Vullo A, Frasconi P.
Packaging by Laszlo Kajan <lkajan@rostlab.org>