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PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites

Florian Gnad, Shubin Ren, Juergen Cox, Jesper V Olsen, Boris Macek, Mario Oroshi and Matthias Mann*

Author Affiliations

Department for Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz, D-82152 Martinsried, Germany

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Genome Biology 2007, 8:R250  doi:10.1186/gb-2007-8-11-r250

Published: 26 November 2007

Additional files

Additional data file 1:

The relative accessibility prediction assigns a value between 0 (fully buried) and 9 (fully exposed) to each residue. For phosphoserines, phosphothreonines and phosphotyrosines, accessibility is significantly higher than for their non-phosphorylated counterparts in the same proteins. The overall accessibility of phosphoproteins is also significantly higher than for a random set of around 1,000 human proteins in Swissprot.

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Additional data file 2:

We visualized determined structures of phosphoproteins via Molsoft ICM Browser Pro (version 3.4-8f).

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Additional data file 3:

Phosphorylation sites located in parts of phosphoproteins that are too flexible for structure determination.

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Additional data file 4:

(a) Conservation of phosphoserine surrounding sequences (green) in comparison to the average conservation of phosphoproteins (red). (b) Conservation of phosphothreonine surrounding sequences (claret-red). (c) Conservation of phosphotyrosine surrounding sequences (yellow). Regions around phosphosites are significantly less likely to be conserved than phosphoproteins on average.

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Additional data file 5:

Optimal parameters for the SVM prediction.

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Additional data file 6:

Prediction accuracies of the SVM approach.

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