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. 2006 Jul 1;34(Web Server issue):W177-81.
doi: 10.1093/nar/gkl266.

DISULFIND: a disulfide bonding state and cysteine connectivity prediction server

Alessio Ceroni  1 , Andrea Passerini, Alessandro Vullo, Paolo Frasconi
Affiliations

DISULFIND: a disulfide bonding state and cysteine connectivity prediction server

Alessio Ceroni et al. Nucleic Acids Res. .

Abstract

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Optionally, disulfide connectivity can be predicted from sequence and a bonding state assignment given as input. The output is a simple visualization of the assigned bonding state (with confidence degrees) and the most likely connectivity patterns. The server is available at http://disulfind.dsi.unifi.it/.

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Figures

Figure 1
Figure 1
Architecture of the bonding state predictor. The lower level provides independent cysteine predictions based on a local kernel kl on local attributes, and a global kernel kg on the entire sequence. The upper level is a BRNN (represented here schematically by its graphical model) that outputs a disulfide-bonding probability p(di) for each cysteine, based on all SVM predictions.
Figure 2
Figure 2
Finite state automaton used in the final stage of bonding state prediction.
Figure 3
Figure 3
Screenshot of the DISULFIND input form.
Figure 4
Figure 4
DISULFIND output.
Figure 5
Figure 5
Accuracy versus rejection rate of the abstaining bonding state predictor for different confidence cutoff values (the rejection rate is the fraction of cysteines that are predicted at a confidence level below the cutoff value shown at the right of each point in the curve).
See this image and copyright information in PMC

References

    1. Fariselli P., Riccobelli P., Casadio R. Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins. Proteins. 1999;36:340–346. - PubMed
    1. Fiser A., Simon I. Predicting the oxidation state of cysteines by multiple sequence alignment. Bioinformatics. 2000;16:251–256. - PubMed
    1. Mucchielli-Giorgi M.H., Hazout S., Tuffèry P. Predicting the disulfide bonding state of cysteines using protein descriptors. Proteins. 2000;46:243–249. - PubMed
    1. Ceroni A., Frasconi P., Passerini A., Vullo A. Predicting the disulfide bonding state of cysteines with combinations of kernel machines. J. VLSI Signal Processing. 2003;35:287–295.
    1. Song J.-N., Wang M.-L., Li W.-J., Xu W.-B. Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition. Biochem. Biophys. Res. Commun. 2004;318:142–147. - PubMed

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