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Protein Characterisation and Prediction Tools
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Summary

This page describes some protein prediction tools freely available on the web.

Probing Protein Sequences

ELM (Eurkaryotic Linear Motif Resource for Functional Sites in Proteins)

Websitehttp://elm.eu.org/

Description:

Scansite

Websitehttp://scansite.mit.edu/
DescriptionA webtool to scan a protein primary sequence for phosphorylation motifs or specific protein binding domains e.g. SH2 domains, 14-3-3 domains or PDZ domains. Protein sequences can be input via database accession number or FASTA format, and batch searches are also possible.

References:

Songyang Z, Blechner S, Hoagland N, Hoekstra MF, Piwnica-Worms H, Cantley LC, Use of an oriented peptide library to determine the optimal substrates of protein kinases, Curr Biol. 1994 Nov 1; 4(11): 973-82.

Yaffe MB, Leparc GG, Lai J, Obata T, Volinia S, Cantley LC, A motif-based profile scanning approach for genome-wide prediction of signaling pathways, Nat Biotechnol. 2001 Apr; 19(4): 348-53.

Obenauer JC, Cantley LC, Yaffe MB, Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs, Nucleic Acids Res. 2003 Jul 1; 31(13): 3635-41.

Phobius - A combined transmembrane topology and signal peptide predictor

Websitehttp://phobius.cbr.su.se/index.html
DescriptionA useful tool for predicting transmembrane domains and signal sequences from a submitted protein primary sequence. Batch searches can also be submitted in Uniprot FASTA format.

References:

Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer. A Combined Transmembrane Topology and Signal Peptide Prediction Method. Journal of Molecular Biology, 338(5):1027-1036, May 2004.

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Protein Characterisation and Prediction Tools