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Open Access Methodology article

A structure filter for the Eukaryotic Linear Motif Resource

Allegra Via14*, Cathryn M Gould2, Christine Gemünd3, Toby J Gibson2* and Manuela Helmer-Citterich1

Author Affiliations

1 Center for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy

2 European Molecular Biology Laboratory, Postfach 10.2209, 69012 Heidelberg, Germany

3 Cellzome AG, Heidelberg, Germany

4 Current address: Biocomputing group, Department of Biochemical Science, Sapienza University of Rome, P.le Aldo Moro 5, Rome, Italy

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BMC Bioinformatics 2009, 10:351  doi:10.1186/1471-2105-10-351

Published: 24 October 2009

Additional files

Additional file 1:

Supplementary information, details and examples. Results for true motifs and random matches taking into account all motif positions (non-wildcard + wildcard). The tables therein reported correspond to tables 1, 2, 3, 4 of the main manuscript. Moreover it describes how neglecting motif wildcard positions improved the initial benchmark set and reports the results of the manual analysis of ten nearly buried instances.

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Additional file 2:

Cumulative distributions in the case all motif position (non-wildcard + wildcard) scores are considered.

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Additional file 3:

ROC curves. The file contains the ROC curves for every type of score (Qacc, Qsse, Qand = Qacc + Qsse) and scheme (i.e. considering both non-wildcard motif position and all motif position scores). The AUC values corresponding to ROC curves of Qacc(all positions), Qsse (all positions) and Qand (all positions) are 0.71, 0.67 and 0.71, respectively.

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Additional file 4:

LM-specific background score distribution plots. Boxplots representing accessibility, secondary structure, and combined background score distributions for each ELM motif.

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Additional file 5:

Correspondences between the x-asis labels of Figure S3 (additional file4) and ELM names.

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Additional file 6:

The ELM dataset of structural instances. The complete set of 158 3D non-redundant instances from 36 different LM entries from the ELM resource release June 2007. The table reports sequence and structure information for each instance.

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