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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)
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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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Interaction Datasets; Extraction; Resource; Negation; Domain; Pdb
ISSN (print) / ISBN
0305-1048
e-ISSN
1362-4962
Journal
Nucleic Acids Research
Quellenangaben
Volume: 42,
Issue: D1,
Pages: D396-D400
Publisher
Oxford University Press
Publishing Place
Oxford
Non-patent literature
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Reviewing status
Peer reviewed