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, 1278, 57-75

Computational Prediction of Protein-Protein Interactions

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Computational Prediction of Protein-Protein Interactions

Tobias Ehrenberger et al. Methods Mol Biol.

Abstract

The prediction of protein-protein interactions and kinase-specific phosphorylation sites on individual proteins is critical for correctly placing proteins within signaling pathways and networks. The importance of this type of annotation continues to increase with the continued explosion of genomic and proteomic data, particularly with emerging data categorizing posttranslational modifications on a large scale. A variety of computational tools are available for this purpose. In this chapter, we review the general methodologies for these types of computational predictions and present a detailed user-focused tutorial of one such method and computational tool, Scansite, which is freely available to the entire scientific community over the Internet.

Figures

Fig. 1
Fig. 1
The results of a high stringency protein scan for all mammalian motifs using the SwissProt protein P53_HUMAN and the default reference proteome are shown. The section entitled “Scan Overview” which summarizes the parameters of the scan of the page is collapsed to better fit this figure on the page
Fig. 2
Fig. 2
The results of a Database Search for ATM in human proteins of SwissProt that are annotated with “cell cycle” and contain the sequence “ARATT”. Here, only one protein matched the given restrictions and this protein also contains the motif that was searched for

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