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

被引：125

作者：

Blohm, Philipp ^{[1
,2
]}

Frishman, Goar ^{[1
]}

Smialowski, Pawel ^{[1
,3
]}

Goebels, Florian ^{[3
]}

Wachinger, Benedikt ^{[1
,2
]}

Ruepp, Andreas ^{[1
]}

Frishman, Dmitrij ^{[1
,3
]}

机构：

[1] HMGU German Res Ctr Environm Hlth, Inst Bioinformat & Syst Biol MIPS, D-85764 Neuherberg, Germany

[2] Clueda AG, D-80687 Munich, Germany

[3] Tech Univ Munich, Dept Genome Oriented Bioinformat, D-85350 Freising Weihenstephan, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / D1期

关键词：

EXTRACTION; NEGATION; DOMAIN; PDB;

D O I：

10.1093/nar/gkt1079

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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%.

引用

页码：D396 / D400

页数：5

共 27 条

[1]

Acland A, 2013, NUCLEIC ACIDS RES, V41, pD8, DOI [10.1093/nar/gkx1095, 10.1093/nar/gks1189, 10.1093/nar/gkq1172]

[2] Biomedical negation scope detection with conditional random fields [J].