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Predicting specificity in bZIP coiled-coil protein interactions

Jessica H Fong1, Amy E Keating2* and Mona Singh1*

Author Affiliations

1 Computer Science Department and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Olden Street, Princeton, NJ 08544, USA

2 Department of Biology, Massachusetts Institute of Technology, Massachusetts Avenue, Cambridge, MA 02139, USA

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Genome Biology 2004, 5:R11  doi:

Published: 16 January 2004


We present a method for predicting protein-protein interactions mediated by the coiled-coil motif. When tested on interactions between nearly all human and yeast bZIP proteins, our method identifies 70% of strong interactions while maintaining that 92% of predictions are correct. Furthermore, cross-validation testing shows that including the bZIP experimental data significantly improves performance. Our method can be used to predict bZIP interactions in other genomes and is a promising approach for predicting coiled-coil interactions more generally.