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. 2007 Jul;35(Web Server issue):W451-4.
doi: 10.1093/nar/gkm296. Epub 2007 May 7.

SH3-Hunter: discovery of SH3 domain interaction sites in proteins

Enrico Ferraro  1 , Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
Affiliations

SH3-Hunter: discovery of SH3 domain interaction sites in proteins

Enrico Ferraro et al. Nucleic Acids Res. 2007 Jul.

Abstract

SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more protein sequences, the server identifies peptides containing poly-proline binding motifs and associates them to a list of SH3 domains, in order to compose peptide-domain pairs. The server can accept a list of peptides and allows users to upload an input file in a proper format. An accurate selection of SH3 domains is available and users can also submit their own SH3 domain sequence. SH3-Hunter evaluates which peptide-domain pair represents a possible interaction pair and produces as output a list of significant interaction sites for each query protein. Each proposed interaction site is associated to a propensity score and sensitivity and precision levels for the prediction. The server prediction capability is based on a neural network model integrating high-throughput pep-spot data with structural information extracted from known SH3-peptide complexes.

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Figures

Figure 1.
Figure 1.
The SH3-Hunter web server. The home page in the background presents the input session characterized by the upload file button and, below, by the text area where the user can paste directly the protein sequences. On the right of the text area, the user can select the peptide filter used to identify putative interacting sites and below the two buttons for scan mode and advanced scan mode represents the two available kinds of submission. The first type of submission allows users to analyze the query sequence checking its interaction propensity with the entire list of SH3-domains of the server (see Table H1 in http://cbm.bio.uniroma2.it/SH3-hunter/help.html). The corresponding output page (on the right) represents a list of significant interaction sites on the query protein with different domains. The last three columns in the output page define respectively the significance (score) and the reliability (sensitivity and precision) of the prediction. On the right side of the table, a graphical representation combines sensitivity and precision levels. Above the results table, two buttons allow users respectively to download the results in a text format and to recover the input page for a new search. The advanced scan submission requires an intermediate session (bottom part in the figure) in which users are required to select one or more among the available SH3 domains. An input text line is also provided for the submission of a user SH3 domain. If a list of proteins is provided in input, one or more of them can be selected for prediction. Then, the scan button submits the chosen peptide–domain pairs to the neural network predictor, thus producing the output list.
See this image and copyright information in PMC

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