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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)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Interaction Datasets; Extraction; Resource; Negation; Domain; Pdb
ISSN (print) / ISBN 0305-1048
e-ISSN 1362-4962
Zeitschrift Nucleic Acids Research
Quellenangaben Band: 42, Heft: D1, Seiten: D396-D400 Artikelnummer: , Supplement: ,
Verlag Oxford University Press
Verlagsort Oxford
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Bioinformatics and Systems Biology (IBIS)