PuSH - Publikationsserver des Helmholtz Zentrums München: Negatome 2.0: A database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis.

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Blohm, P. ; Frishman, G. ; Smialowski, P. ; Goebels, F.* ; Wachinger, B. ; Ruepp, A. ; Frishman, D.

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

Nucleic Acids Res. 42, D396-D400 (2014)

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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 http://mips.helmholtz-muenchen.de/proj/ppi/negatome). 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%.

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