BIND: the Biomolecular Interaction Network Database

By Gary D. Bader, Ian M. Donaldson, Cheryl Wolting, B. F. Ouellette, Tony Pawson, Christopher W. V. Hogue. Nucleic Acids Res., 2003

1,294 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/42a77b1006675dc954495459ba3bf9c194258c04

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Citations in the corpus

Extracting interactions between proteins from the literature (2008, positive): “All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published articles www.hprd.org HPID Human Protein Interaction Database integrates the protein interactions in BIND, DIP and HPRD www.hpid.org IntAct IntAct consists o”
Improved human disease candidate gene prioritization using mouse phenotype (2007, methodology): “This data set contained 8,040 distinct genes from 19,714 distinct interaction complexes from 3 interaction databases: HPRD [47], BIND [48], and BioGRID [49].”
An experimentally derived confidence score for binary protein-protein interactions (2008, neutral): “Because there is no available gold standard for non-interacting proteins and because randomly chosen protein pairs are unlikely a priori to interact, our RRS serves as a negative control set.”
The Database of Interacting Proteins: 2004 update (2004, background): “It is expected to be supported by the major providers of protein interaction data, including DIP, BIND (15) and Mint (16) databases.”
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions (2002, background): “(1) would, at a little overhead to the experimentalist, significantly increase the rate of incorporation of novel data into protein interaction databases.”
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists (2007, background): “The first was to compare the kappa score distribution of every possible pair of human genes (approximately 300 million pairs) to that of reported human protein-protein interaction pairs [34].”
IFITM Proteins Mediate the Innate Immune Response to Influenza A H1N1 Virus, West Nile Virus and Dengue Virus (2009, background): “, 2005), The Biomolecular Interaction Network Database (Bader et al., 2001) and BioGrid (Stark et al.”
Mining literature for protein-protein interactions (2001, background): “Already, databases of protein–protein interactions (Xenarios et al., 2001; Bader et al., 2001) and signaling pathways (Kanehisa and Goto, 2000; the Signal Transduction Knowledge Environment: http://www.171.66.122.61/) are generating new insights * These authors contributed equally to this work.…”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, methodology): “Scoring of tentative PI from the LCMS and MALDI assays was conducted using a logistic regression model using reference PI obtained by low-throughput experiments curated in the DIP, BIND, and IntAct databases [35–37] as a positive training set.”
Algorithms for Detecting Significantly Mutated Pathways in Cancer (2010, positive): “Instead, building on an idea presented in Kirsch et al. (2009), we develop a two-stage test for our problem that allows us to ﬂag a number of subnetworks in our data as statistically signiﬁcant with small FDR values.”
Cytoscape: a software environment for integrated models of biomolecular interaction networks. (2003, neutral): “databases such as BIND (Bader et al. 2001), DIP (Xenarios and Eisenberg 2001), or TRANSFAC (Wingender et al.”
CORUM: the comprehensive resource of mammalian protein complexes—2009 (2007, methodology): “Bioinformatics analyses of the mammalian complexome can be performed either by using artiﬁcially constructed protein complexes (10) or data from manually curated datasets (11,12).”
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions (2016, background): “Consequently, public databases for human-specific molecular interaction data have been undergoing a rapid growth within the past decade, such as BIND [18], DIP [19], STITCH [20], HPRD [21], TTD [22], DrugBank [23], ChEMBL [24], KEGG [25], BindingDB [26], SuperTarget and Matador [27], to name a few.”
Disease candidate gene identification and prioritization using protein interaction networks (2009, methodology): “Human protein interaction datasets The human protein interaction dataset (file "interactions.gz"), a compilation of PPIs from BIND [ 44 ], BioG-RID [45], and HPRD [46], was downloaded from NCBI Entrez Gene FTP site [43].”
STRING: known and predicted protein–protein associations, integrated and transferred across organisms (2004, background): “are directly imported from databases (2,5,17), and given a uniform confidence score per dataset.”
Reactome: a knowledgebase of biological pathways (2004, neutral): “This will also enable data exchange with other pathway databases, such as the Cycs (7), KEGG (8) and amaze (9), and molecular interaction databases, such as BIND (10) and HPRD (11).”