The Biomolecular Interaction Network Database and related tools 2005 update

By C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, Doron Betel, B. Bobechko, K. Boutilier, E. Burgess and 64 more. Nucleic Acids Res., 2004

636 citations recorded by the source corpus.

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues.

Subfields: Molecular Biology

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Citations in the corpus

STRING 8—a global view on proteins and their functional interactions in 630 organisms (2008, background): “Apart form the resources already included in the previous release [MINT (10), HPRD (9), BIND (12), DIP (11), BioGRID (8), KEGG (13) and Reactome (14)], a number of resources have been newly included [IntAct (7), EcoCyc (15), NCI-Nature Pathway Interaction Database and Gene Ontology (GO) protein comp”
ModBase, a database of annotated comparative protein structure models and associated resources (2013, methodology): “A comparison of the predicted interactions to experimental results in the BIND database ( 30 ) reveals an overlap of 3%. The predictions are assigned confidence levels (Z-scores) that may be used to produce a list of testable hypotheses about interacting proteins.”
IntAct—open source resource for molecular interaction data (2006, neutral): “To share the curation workload, avoid redundant curation and ensure consistency in annotation policies, five public databases, BIND (14), MINT (15), DIP (16), MPact (17) and IntAct, have formed the IMEx consortium (IMEx—http://imex.”
How complete are current yeast and human protein-interaction networks? (2006, methodology): “…assays may be biased toward interactions between abundant proteins, and *This interaction assay false-positive rate is derived using the method of D’haeseleer and Church [32] and a reference set of 20,296 unique interactions from HPRD [54], BIND [55], Reactome [56], and Ramani et al. [49].”
STRING 7—recent developments in the integration and prediction of protein interactions (2006, methodology): “Known interactions in STRING are primarily imported from existing excellent interaction databases (1–5,8,9), and are complemented by automated text mining of PubMed abstracts and several other bodies of scientiﬁc text [such as from Ref.”
GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy *S (2008, methodology): “The human experimental protein-protein interaction (PPI) data were derived from the Database of Interacting Proteins (DIP) (31), BioGrid (32), the Molecular Interaction Database (MINT) (33), the Biomolecular Interaction Network Database (BIND) (34), and the Human Protein Reference Database (HPRD) (3”
iRefIndex: A consolidated protein interaction database with provenance (2008, methodology): “Inter-action databases included BIND [22,23], BioGRID [24], DIP [25], HPRD [26,27], IntAct [28,29], MINT [30], MPact [31], MPPI [32] and OPHID [33].”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, result): “A comparison of the predicted interactions to experimental results in the BIND database (30) reveals an overlap of 3%.”
Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases (2007, background): “Unlike other structurebased databases, domain interactions are grouped by geometry into conserved interaction modes for each pair of domain families across all PDB structures [26].”
TALE: A Tool for Approximate Large Graph Matching (2008, methodology): “For the results presented here, the parameter settings are: Sbit = 96, ρ = 25% and Pimp = 15% for the BIND dataset, and Sbit = 32, ρ = 25% and Pimp = 25% for the ASTRAL dataset.”
BisoGenet: a new tool for gene network building, visualization and analysis (2010, methodology): “Protein-protein and protein-DNA interactions information is taken from the Database of Interacting Proteins DIP[3], BIND[4], the Human Protein Reference Database HPRD[5], the Molecular INTeraction database MINT[7], Intact[8] and Bio-Grid[6].”