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

Philipp Blohm, Goar Frishman, Pawel Smialowski, Florian Goebels, Benedikt Wachinger, Andreas Ruepp, Dmitrij Frishman

Research output: Contribution to journalArticlepeer-review

114 Scopus citations

Abstract

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%.

Original languageEnglish
Pages (from-to)D396-D400
JournalNucleic Acids Research
Volume42
Issue numberD1
DOIs
StatePublished - 1 Jan 2014

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