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BindingDB: A Web-Accessible Molecular Recognition Database
Abstract
This paper presents an initial description of the BindingDB, a public web-accessible database of measured binding affinities for various molecular types (http://www.bindingdb.org). The BindingDB allows queries based upon a range of criteria, including chemical similarity or substructure, sequence homology, numerical criteria (e.g. delta G(o) < 5 kcal/mol) and reactant names (e.g. "lysozyme"). Principles of Human-Computer Interactions are being employed in creating the query interface and user-feedback is being solicited. The data specification includes significant experimental detail. A full dictionary has been created for isothermal titration calorimetry data in consultation with experimentalists and data dictionaries for enzyme-inhibition and other measurement techniques are being developed. Currently, the BindingDB contains several data sets of broad interest, such as antigen-antibody binding and cyclodextrin/small molecule binding. However, it is anticipated that online deposition by experimentalists will ultimately contribute to a larger flow of data. We are actively developing software and file specifications to facilitate such deposition.
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Cited by
Gilson, M. K., Liu, T., Baitaluk, M., Nicola, G., Hwang, L., & Chong, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1072 · Cited by 1,628
Self-citationThe PDBbind database: methodologies and updates
Wang, R., Fang, X., Lu, Y., Yang, C.-Y., & Wang, S. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm048957q · Cited by 933
Reymond, J.-L. (2015) · Accounts of Chemical Research · doi:10.1021/ar500432k · Cited by 720
Virtual Screening Strategies in Drug Discovery: A Critical Review
Lavecchia, A., & Giovanni, C. (2013) · Current Medicinal Chemistry · doi:10.2174/09298673113209990001 · Cited by 686
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Himmelstein, D. S., Lizee, A., Hessler, C., Brueggeman, L., Chen, S. L., Hadley, D., Green, A., Khankhanian, P., & Baranzini, S. E. (2017) · eLife · doi:10.7554/elife.26726 · Cited by 666
Metadata
- Authors
- Chen, X., Liu, M., & Gilson, M.
- Venue
- Combinatorial Chemistry & High Throughput Screening
- Publisher
- Bentham Science Publishers Ltd.
- Published
- 2001-12-01
- Volume
- 4
- Issue
- 8
- Pages
- 719-725
- ISSN
- 1386-2073 (ISSN-L)
- OpenAlex
- W2111078532
- Cited by
- 223
- References
- 0
- FWCI
- 3.46
- Type
- journal article
- Language
- en
- Open access
- closed
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- Chen, X., Liu, M., & Gilson, M. (2001). BindingDB: A Web-Accessible Molecular Recognition Database. Combinatorial Chemistry & High Throughput Screening. https://doi.org/10.2174/1386207013330670
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