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Bioinformatics. 2014 Sep 15;30(18):2668-9. doi: 10.1093/bioinformatics/btu350. Epub 2014 May 28.

MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions.

Author information

1
Bioinformatics Group, Department of Computer Science, 79110 Freiburg and Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany.
2
Bioinformatics Group, Department of Computer Science, 79110 Freiburg and Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany Bioinformatics Group, Department of Computer Science, 79110 Freiburg and Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany.

Abstract

MoDPepInt (Modular Domain Peptide Interaction) is a new easy-to-use web server for the prediction of binding partners for modular protein domains. Currently, we offer models for SH2, SH3 and PDZ domains via the tools SH2PepInt, SH3PepInt and PDZPepInt, respectively. More specifically, our server offers predictions for 51 SH2 human domains and 69 SH3 human domains via single domain models, and predictions for 226 PDZ domains across several species, via 43 multidomain models. All models are based on support vector machines with different kernel functions ranging from polynomial, to Gaussian, to advanced graph kernels. In this way, we model non-linear interactions between amino acid residues. Results were validated on manually curated datasets achieving competitive performance against various state-of-the-art approaches.

AVAILABILITY AND IMPLEMENTATION:

The MoDPepInt server is available under the URL http://modpepint.informatik.uni-freiburg.de/.

PMID:
24872426
PMCID:
PMC4155253
DOI:
10.1093/bioinformatics/btu350
[Indexed for MEDLINE]
Free PMC Article

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