DOKK / manpages / debian 10 / disulfinder / disulfinder.1.en

disulfinder - cysteines disulfide bonding state and connectivity predictor

disulfinder [OPTIONS]

'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.

For the disulphide connectivity predictor see:

For the cystein bonding state predictor see:

alternative connectivity patterns (default=3)
output dir where predictions will be saved (default=$PWD)
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.
work directory (default=~/disulfinder)
package data directory containing Models (default=/usr/share/disulfinder)
output format type (default=ascii)
blastpgp -d option (default=/data/sp+trembl)
cleanup intermediate prediction files (default=false)
use pssm instead of counts for profiles (default=false)
assume bonding state is known (one file for each chain in directory <rootdir>/Predictions/Bondstate/Viterbi) (default=false)
disulfinder version
-?, --help
help screen

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

default package data directory
default work directory

The work directory is not cleaned up automatically.

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

Packaging by Laszlo Kajan <>


2018-09-23 1.2.11