@Article{Kundu_Mann_Costa-MoDPe_inter_web-2014,
  author =	 {Kundu, Kousik and Mann, Martin and Costa, Fabrizio and 
                  Backofen, Rolf},
  title =	 {{MoDPepInt}: an interactive web server for prediction of 
                  modular domain-peptide interactions},
  journal =	 {Bioinformatics},
  year =	 {2014},
  volume =	 {30},
  number =	 {18},
  pages =	 {2668-2669},
  user =	 {kousik},
  pmid =	 {24872426},
  doi = 	 {10.1093/bioinformatics/btu350},
  issn = 	 {1367-4811},
  issn = 	 {1367-4803},
  abstract =	 {SUMMARY:: 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/ CONTACT: : 
                  backofen@informatik.uni-freiburg.de Supplementary 
                  information: Supplementary data are available at 
                  Bioinformatics online.}
}