Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

Nucleic Acids Res. 2014 Jan;42(Database issue):D396-400. doi: 10.1093/nar/gkt1079. Epub 2013 Nov 8.


Knowledge about non-interacting proteins (NIPs) is important for training the algorithms to predict protein-protein interactions (PPIs) and for assessing the false positive rates of PPI detection efforts. We present the second version of Negatome, a database of proteins and protein domains that are unlikely to engage in physical interactions (available online at Negatome is derived by manual curation of literature and by analyzing three-dimensional structures of protein complexes. The main methodological innovation in Negatome 2.0 is the utilization of an advanced text mining procedure to guide the manual annotation process. Potential non-interactions were identified by a modified version of Excerbt, a text mining tool based on semantic sentence analysis. Manual verification shows that nearly a half of the text mining results with the highest confidence values correspond to NIP pairs. Compared to the first version the contents of the database have grown by over 300%.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Data Mining
  • Databases, Protein*
  • Internet
  • Molecular Sequence Annotation
  • Protein Conformation
  • Protein Interaction Domains and Motifs*
  • Protein Interaction Mapping*