BIND--The Biomolecular Interaction Network Database
- PMID: 11125103
- PMCID: PMC29820
- DOI: 10.1093/nar/29.1.242
BIND--The Biomolecular Interaction Network Database
Abstract
The Biomolecular Interaction Network Database (BIND; http://binddb. org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND 2.0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed of proteins, nucleic acids and small molecules. Chemical reactions, photochemical activation and conformational changes can also be described. Everything from small molecule biochemistry to signal transduction is abstracted in such a way that graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for kinetic simulations. BIND anticipates the coming large influx of interaction information from high-throughput proteomics efforts including detailed information about post-translational modifications from mass spectrometry. Version 2.0 of the BIND data model is discussed as well as implementation, content and the open nature of the BIND project. The BIND data specification is available as ASN.1 and XML DTD.
Figures
Similar articles
-
BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways.Bioinformatics. 2000 May;16(5):465-77. doi: 10.1093/bioinformatics/16.5.465. Bioinformatics. 2000. PMID: 10871269
-
BIND: the Biomolecular Interaction Network Database.Nucleic Acids Res. 2003 Jan 1;31(1):248-50. doi: 10.1093/nar/gkg056. Nucleic Acids Res. 2003. PMID: 12519993 Free PMC article.
-
Automatic annotation of BIND molecular interactions from three-dimensional structures.Biopolymers. 2001-2002;61(2):111-20. doi: 10.1002/1097-0282(2001/2002)61:2<111::AID-BIP10143>3.0.CO;2-8. Biopolymers. 2001. PMID: 11987160
-
Assembly of cell regulatory systems through protein interaction domains.Science. 2003 Apr 18;300(5618):445-52. doi: 10.1126/science.1083653. Science. 2003. PMID: 12702867 Review.
-
Biomolecular halogen bonds.Top Curr Chem. 2015;358:241-76. doi: 10.1007/128_2014_551. Top Curr Chem. 2015. PMID: 25326832 Review.
Cited by
-
Heterogeneous network approaches to protein pathway prediction.Comput Struct Biotechnol J. 2024 Jun 27;23:2727-2739. doi: 10.1016/j.csbj.2024.06.022. eCollection 2024 Dec. Comput Struct Biotechnol J. 2024. PMID: 39035835 Free PMC article. Review.
-
In Silico Analysis of Protein-Protein Interactions of Putative Endoplasmic Reticulum Metallopeptidase 1 in Schizosaccharomyces pombe.Curr Issues Mol Biol. 2024 May 12;46(5):4609-4629. doi: 10.3390/cimb46050280. Curr Issues Mol Biol. 2024. PMID: 38785548 Free PMC article.
-
Identify Biomarkers and Design Effective Multi-Target Drugs in Ovarian Cancer: Hit Network-Target Sets Model Optimizing.Biology (Basel). 2022 Dec 19;11(12):1851. doi: 10.3390/biology11121851. Biology (Basel). 2022. Retraction in: Biology (Basel). 2024 Jan 30;13(2):86. doi: 10.3390/biology13020086. PMID: 36552360 Free PMC article. Retracted.
-
Systems Drug Design for Muscle Invasive Bladder Cancer and Advanced Bladder Cancer by Genome-Wide Microarray Data and Deep Learning Method with Drug Design Specifications.Int J Mol Sci. 2022 Nov 10;23(22):13869. doi: 10.3390/ijms232213869. Int J Mol Sci. 2022. PMID: 36430344 Free PMC article.
-
Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel). 2022 Oct 5;11(19):2614. doi: 10.3390/plants11192614. Plants (Basel). 2022. PMID: 36235479 Free PMC article. Review.
References
-
- Mendelsohn A.R. and Brent,R. (1999) Protein interaction methods–toward an endgame. Science, 284, 1948–1950. - PubMed
-
- Cassman M., Hunter,T. and Pawson,T. (2000) Proteins suggest form of their own database. Nature, 403, 591–592. - PubMed
-
- Pawson T. (1995) Protein modules and signalling networks. Nature, 373, 573–580. - PubMed
-
- Ostell J. and Kans,J.A. (1998) In Baxevanis,A.D. and Ouellette,B.F. (eds), Bioinformatics, A Practical Guide to the Analysis of Genes and Proteins. John Wiley and Sons, New York, NY. Vol. 39, pp. 121–144.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases