The Negatome database: a reference set of non-interacting protein pairs

Nucleic Acids Res. 2010 Jan;38(Database issue):D540-4. doi: 10.1093/nar/gkp1026. Epub 2009 Nov 17.


The Negatome is a collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions. The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analyzing protein complexes with known 3D structure. More stringent lists of non-interacting pairs were derived from these two datasets by excluding interactions detected by high-throughput approaches. Additionally, non-interacting protein domains have been derived from the stringent manual and structural data, respectively. The Negatome is much less biased toward functionally dissimilar proteins than the negative data derived by randomly selecting proteins from different cellular locations. It can be used to evaluate protein and domain interactions from new experiments and improve the training of interaction prediction algorithms. The Negatome database is available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Computational Biology / methods*
  • Computational Biology / trends
  • Databases, Genetic*
  • Databases, Nucleic Acid*
  • Databases, Protein
  • Genome, Fungal
  • Humans
  • Information Storage and Retrieval / methods
  • Internet
  • Protein Interaction Mapping*
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Saccharomyces cerevisiae / metabolism
  • Software


  • Proteins