The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology
Open accessAbstract
BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,578
Weininger, D. (1988) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00057a005 · Cited by 7,436
The Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605
UniProt: a hub for protein information
The UniProt Consortium (2015) · Nucleic Acids Research · doi:10.1093/nar/gku989 · Cited by 5,106
ZINC: A Free Tool to Discover Chemistry for Biology
Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci3001277 · Cited by 2,509
Relating protein pharmacology by ligand chemistry
Keiser, M. J., Roth, B. L., Armbruster, B. N., Ernsberger, P., Irwin, J. J., & Shoichet, B. K. (2007) · Nature Biotechnology · doi:10.1038/nbt1284 · Cited by 2,402
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
Liu, T., Lin, Y., Wen, X., Jorissen, R. N., & Gilson, M. K. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl999 · Cited by 2,124
Self-citationDrugBank 4.0: shedding new light on drug metabolism
Law, V., Knox, C., Djoumbou, Y., Jewison, T., Guo, A. C., Liu, Y., Maciejewski, A., Arndt, D., Wilson, M., Neveu, V., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1068 · Cited by 1,993
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Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1033 · Cited by 3,249
ChEMBL: towards direct deposition of bioassay data
Mendez, D., Gaulton, A., Bento, A. P., Chambers, J., De Veij, M., Félix, E., Magariños, M. P., Mosquera, J. F., Mutowo, P., Nowotka, M., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1075 · Cited by 2,372
Gaulton, A., Hersey, A., Nowotka, M., Bento, A. P., Chambers, J., Mendez, D., Mutowo, P., Atkinson, F., Bellis, L. J., Cibrián-Uhalte, E., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1074 · Cited by 2,330
The rise of deep learning in drug discovery
Chen, H., Engkvist, O., Wang, Y., Olivecrona, M., & Blaschke, T. (2018) · Drug Discovery Today · doi:10.1016/j.drudis.2018.01.039 · Cited by 1,770
Oughtred, R., Rust, J., Chang, C., Breitkreutz, B., Stark, C., Willems, A., Boucher, L., Leung, G., Kolas, N., Zhang, F., et al. (2021) · Protein Science · doi:10.1002/pro.3978 · Cited by 1,858
Metadata
- Authors
- Gilson, M. K., Liu, T., Baitaluk, M., Nicola, G., Hwang, L., & Chong, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-10-19
- Volume
- 44
- Issue
- D1
- Pages
- D1045-D1053
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2204695023
- Cited by
- 1,628
- References
- 37
- FWCI
- 64.22
- Type
- journal article
- Language
- en
- Open access
- gold
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- Gilson, M. K., Liu, T., Baitaluk, M., Nicola, G., Hwang, L., & Chong, J. (2016). BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Research. https://doi.org/10.1093/nar/gkv1072
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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