swMATH ID: 29347
Software Authors: Blohm P, Frishman G, Smialowski P et al
Description: The Negatome Database 2.0. The Negatome is a collection of protein and domain pairs which are unlikely engaged in direct physical interactions. The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analysing protein complexes from the PDB. More stringent lists of non-interacting pairs were derived from these two datasets by excluding interactions from IntAct. It can be used to evaluate newly derived experimental interactions. The Negatome is much less biased towards functionally dissimilar proteins than the negative data derived by randomly selecting proteins from different cellular locations. Thus, the negatome is complementary to such random data for training protein interaction prediction algorithms. Negatome 2.0 was created by use of an advanced text mining procedure to guide the manual annotation process. Potential non-interactions were proposed by a modified version of a text mining tool called Excerbt. Compared to the first version the contents of the database have grown by over 300
Homepage: http://mips.helmholtz-muenchen.de/proj/ppi/negatome/
Related Software: STRINGdb; ANIMO; PRS; NET-SYNTHESIS; SMPDB; PathCellNet; GNAT; YEASTRACT; ATtRACT; COMPARTMENTS; PaxDb; MOPED; IDDI; DOMINE; ProtNet; inSilicoMerging; RTCGA; WikiPathways; NPInter; miRTarBase
Referenced in: 2 Publications

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