Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Jul 1;34(Web Server issue):W169-72.
doi: 10.1093/nar/gkl208.

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

Mauro Amico  1 , Michele Finelli, Ivan Rossi, Andrea Zauli, Arne Elofsson, Håkan Viklund, Gunnar von Heijne, David Jones, Anders Krogh, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
Affiliations

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

Mauro Amico et al. Nucleic Acids Res. .

Abstract

The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating metazoan genomes (http://www.biosapiens.info). In this context, the PONGO DAS server (http://pongo.biocomp.unibo.it) provides the annotation on predictive basis for the all-alpha membrane proteins in the human genome, not only through DAS queries, but also directly using a simple web interface. In order to produce a more comprehensive analysis of the sequence at hand, this annotation is carried out with four selected and high scoring predictors: TMHMM2.0, MEMSAT, PRODIV and ENSEMBLE1.0. The stored and pre-computed predictions for the human proteins can be searched and displayed in a graphical view. However the web service allows the prediction of the topology of any kind of putative membrane proteins, regardless of the organism and more importantly with the same sequence profile for a given sequence when required. Here we present a new web server that incorporates the state-of-the-art topology predictors in a single framework, so that putative users can interactively compare and evaluate four predictions simultaneously for a given sequence. Together with the predicted topology, the server also displays a signal peptide prediction determined with SPEP. The PONGO web server is available at http://pongo.biocomp.unibo.it/pongo.

PubMed Disclaimer

Figures

Figure 1
Figure 1
The PONGO homepage. On the left-side it is possible to follow the status of the different queries and the starting of a new action.
Figure 2
Figure 2
An example of PONGO results for a protein chain endowed with a signal peptide.
See this image and copyright information in PMC

References

    1. Casadio R., Fariselli P., Martelli P.L. In silico prediction of the structure of membrane proteins: is it feasible? Brief. Bioinf. 2003;4:341–348. - PubMed
    1. Taylor P.D., Attwood T.K., Flower D.R. BPROMPT: a consensus server for membrane protein prediction. Nucleic Acids Res. 2003;31:3698–3700. - PMC - PubMed
    1. Arai M., Mitsuke H., Ikeda M., Xia J.-X., Kikuchi T., Satake M., Shimizu T. ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res. 2004;32:W390–W393. - PMC - PubMed
    1. Jones D.T., Taylor W.R., Thornton J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 1994;15:3038–3049. - PubMed
    1. Krogh A., Larsson B., von Heijne G., Sonnhammer E.L.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 2001;305:567–580. - PubMed

Publication types

Substances