Predicting specificity in bZIP coiled-coil protein interactions

Genome Biol. 2004;5(2):R11. doi: 10.1186/gb-2004-5-2-r11. Epub 2004 Jan 16.

Abstract

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.

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Basic-Leucine Zipper Transcription Factors
  • Computational Biology / methods*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Fungal Proteins / chemistry
  • Fungal Proteins / metabolism
  • G-Box Binding Factors
  • Humans
  • Models, Molecular
  • Protein Binding
  • Protein Structure, Secondary
  • Reproducibility of Results
  • Static Electricity
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism

Substances

  • Basic-Leucine Zipper Transcription Factors
  • DNA-Binding Proteins
  • Fungal Proteins
  • G-Box Binding Factors
  • Transcription Factors