The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.
Thera-SAbDab: the Therapeutic Structural Antibody Database
Open accessPublished version of a preprint
Abstract
The Therapeutic Structural Antibody Database (Thera-SAbDab; http://opig.stats.ox.ac.uk/webapps/therasabdab) tracks all antibody- and nanobody-related therapeutics recognized by the World Health Organisation (WHO), and identifies any corresponding structures in the Structural Antibody Database (SAbDab) with near-exact or exact variable domain sequence matches. Thera-SAbDab is synchronized with SAbDab to update weekly, reflecting new Protein Data Bank entries and the availability of new sequence data published by the WHO. Each therapeutic summary page lists structural coverage (with links to the appropriate SAbDab entries), alignments showing where any near-matches deviate in sequence, and accompanying metadata, such as intended target and investigated conditions. Thera-SAbDab can be queried by therapeutic name, by a combination of metadata, or by variable domain sequence - returning all therapeutics that are within a specified sequence identity over a specified region of the query. The sequences of all therapeutics listed in Thera-SAbDab (461 unique molecules, as of 5 August 2019) are downloadable as a single file with accompanying metadata.
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“As of July 2022, this database is tracking 748 unique therapeutics, including monoclonal antibody and bispecific therapeutics.”
From Computational and artificial intelligence-based methods for antibody development (2023) · cites this paper as [15]
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“Additionally, the Therapeutic Structural Antibody Database (Thera-SAbDab) is a therapeutic structural antibody database including antibody-and nanobodyrelated biotherapeutics [15].”
From Computational and artificial intelligence-based methods for antibody development (2023) · cites this paper as [15]
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Citations
Cites
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“These fragments can be expressed in dimeric form to improve avidity, or conjugated with polyethylene glycol (‘pegylated’) for slower clearance (4), with radioisotopes for diagnostic purposes (5), or with radioisotopes or noxious small molecules/peptides for cytotoxicity (6).”
BackgroundBispecific antibodies: a mechanistic review of the pipeline
Labrijn, A. F., Janmaat, M. L., Reichert, J. M., & Parren, P. W. H. I. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-019-0028-1 · Cited by 1,303 · cited 1×
“As of June 2019, bispecific mAbs, linked Fabs, linked scFvs and linked single-domain variable fragments have all been assessed in clinical trials (7).”
BackgroundStandard conformations for the canonical structures of immunoglobulins 1 1Edited by I. A. Wilson
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SAbDab: the structural antibody database
Dunbar, J., Krawczyk, K., Leem, J., Baker, T., Fuchs, A., Georges, G., Shi, J., & Deane, C. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1043 · Cited by 674 · cited 2×
“A significant fraction of these structures contain antibody variable domains, and these are recorded by the Structural Antibody Database (SAbDab (16); 7184 variable domain structures over 3663 PDB entries as of 5 August 2019).”
BackgroundNanobodies as therapeutics: big opportunities for small antibodies
Steeland, S., Vandenbroucke, R. E., & Libert, C. (2016) · Drug Discovery Today · doi:10.1016/j.drudis.2016.04.003 · Cited by 476
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“Whole monoclonal antibody (mAb) therapies dominate the industry - drugs that mimic natural antibodies by containing two identical variable domain structures with a particular specificity (3).”
BackgroundANARCI: antigen receptor numbering and receptor classification
Dunbar, J., & Deane, C. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv552 · Cited by 421 · cited 3×
“We harvest sequences as they are released by the WHO, number them with ANARCI (17), and perform a weekly sequence alignment of all therapeutic variable domain sequences to the sequences of known structures stored in SAbDab.”
BackgroundMethodInfluentialHomology modeling in drug discovery: Overview, current applications, and future perspectives
Muhammed, M. T., & Aki, E. (2018) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13388 · Cited by 381 · cited 1×
“It can also assist subsequent development and optimization, as homology models of mutants derived from a known structure are in general more accurate than those for which no close structural partner is available (14).”
BackgroundFive computational developability guidelines for therapeutic antibody profiling
Raybould, M. I. J., Marks, C., Krawczyk, K., Taddese, B., Nowak, J., Lewis, A. P., Bujotzek, A., Shi, J., & Deane, C. M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810576116 · Cited by 357 · cited 2×
“Links to appropriate SAbPred (21) informatics tools (such as ABodyBuilder (22) for variable domain structure modelling, and TAP (18) for developability assessment) are also provided.”
BackgroundMethodABodyBuilder: automated antibody structure prediction with data-driven accuracy estimation
Leem, J., Dunbar, J., Georges, G., Shi, J., & Deane, C. M. (2016) · mAbs · doi:10.1080/19420862.2016.1205773 · Cited by 238 · cited 1×
“Links to appropriate SAbPred (21) informatics tools (such as ABodyBuilder (22) for variable domain structure modelling, and TAP (18) for developability assessment) are also provided.”
MethodSAbPred: a structure-based antibody prediction server
Dunbar, J., Krawczyk, K., Leem, J., Marks, C., Nowak, J., Regep, C., Georges, G. J., Kelm, S., Popovic, B., & Deane, C. M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw361 · Cited by 202 · cited 1×
“Links to appropriate SAbPred (21) informatics tools (such as ABodyBuilder (22) for variable domain structure modelling, and TAP (18) for developability assessment) are also provided.”
MethodAntibody-Radionuclide Conjugates for Cancer Therapy: Historical Considerations and New Trends
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“These fragments can be expressed in dimeric form to improve avidity, or conjugated with polyethylene glycol (‘pegylated’) for slower clearance (4), with radioisotopes for diagnostic purposes (5), or with radioisotopes or noxious small molecules/peptides for cytotoxicity (6).”
BackgroundStructure-based drug design: aiming for a perfect fit
van Montfort, R. L. M., & Workman, P. (2017) · Essays in Biochemistry · doi:10.1042/ebc20170052 · Cited by 127 · cited 1×
“Structural knowledge about both the intended target and the therapeutic lead compound is of high importance for rational drug discovery (12,13).”
BackgroundThe ABCD database: a repository for chemically defined antibodies
de Lima, W. C., Gasteiger, E., Marcatili, P., Duek, P. D., Bairoch, A., & Cosson, P. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz714 · Cited by 70 · cited 1×
“For example, the recently published ABCD database provides antibody synonyms, antigen UniProt links and publication references (11).”
BackgroundBenschop, R. J., Chow, C.-K., Tian, Y., Nelson, J., Barmettler, B., Atwell, S., Clawson, D. K., Chai, Q., Jones, B. E., Fitchett, J. R., et al. (2019) · mAbs · doi:10.1080/19420862.2019.1624463 · Cited by 53 · cited 12×
“A significant fraction of these structures contain antibody variable domains, and these are recorded by the Structural Antibody Database (SAbDab (16); 7047 variable domain structures over 3620 PDB entries as of 18th July 2019).”
BackgroundInfluentialPEGylation of Antibody Fragments for Half-Life Extension
Jevševar, S., Kusterle, M., & Kenig, M. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-931-0_15 · Cited by 38
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Raybould, M. I. J., Wong, W. K., & Deane, C. M. (2019) · Molecular Systems Design & Engineering · doi:10.1039/c9me00034h · Cited by 14 · cited 1×
“Structural knowledge about both the intended target and the therapeutic lead compound is of high importance for rational drug discovery (12,13).”
Background
Flagged first, then by citations
Research works printed but not linked: 3
- WHO, 2018, Proposed International Nonproprietary Names (INN) List 120, WHO Drug Information, 32, 559
- WHO, 2019, Recommended International Nonproprietary Names (INN) List 81, WHO Drug Information, 33, 59
- Poiron, 2010, IMGT/mAb-DB: the IMGT database for therapeutic monoclonal antibodies, JOBIM 2010, 13, 470b
Cited by
Sorted by citations
Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P., Crichlow, G. V., Dalenberg, K., Duarte, J. M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1077 · Cited by 926
“Thera-SAbDab (94) Therapeutic Structural Antibody Database”
Efficient evolution of human antibodies from general protein language models
Hie, B., Shanker, V. R., Xu, D., Bruun, T. U. J., Weidenbacher, P. A. B., Tang, S., Wu, W. C. H., Pak, J. E., & Kim, P. S. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01763-2 · Cited by 472
“We downloaded 742 therapeutically relevant antibodies from the Thera-SAbDab database as of 26 February 2022 (http://opig.stats. ox.ac.uk/webapps/newsabdab/therasabdab/) 47 .”
Prihoda, D., Maamary, J., Waight, A., Juan, V., Fayadat-Dilman, L., Svozil, D., & Bitton, D. A. (2022) · mAbs · doi:10.1080/19420862.2021.2020203 · Cited by 190
“Recovering 152 putative parental sequences Records with “-zumab” suffix were collected from TheraSAbDab, totaling 164 humanized therapeutics.”
MethodComputational and artificial intelligence-based methods for antibody development
Kim, J., McFee, M., Fang, Q., Abdin, O., & Kim, P. M. (2023) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2022.12.005 · Cited by 178
IgLM: Infilling language modeling for antibody sequence design
Shuai, R. W., Ruffolo, J. A., & Gray, J. J. (2023) · Cell Systems · doi:10.1016/j.cels.2023.10.001 · Cited by 191
Metadata
- Authors
- Raybould, M. I. J., Marks, C., Lewis, A. P., Shi, J., Bujotzek, A., Taddese, B., & Deane, C. M.
- Affiliations
- University of Oxford (GB)
- GlaxoSmithKline (United Kingdom) (GB)
- UCB Pharma (United Kingdom) (GB)
- Roche Pharma AG (Germany) (DE)
- AstraZeneca (United Kingdom) (GB)
- Corresponding author
- Deane, Charlotte M
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-09-26
- Volume
- 48
- Issue
- D1
- Pages
- D383-D388
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6943036
- OpenAlex
- W2974982237
- Cited by
- 199
- References
- 19
- Citations by year
- 2026: 29 · 2025: 55 · 2024: 41 · 2023: 27 · 2022: 23 · 2021: 19 · 2020: 4 · 2019: 1
- FWCI
- 7.77
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Engineering and Physical Sciences Research Council
- Medical Research Council (EP/L016044/1)
- GlaxoSmithKline plc.
- AstraZeneca plc
- F. Hoffmann-La Roche
- UCB Celltech
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- therapeutic antibodies, nanobodies, antibody variable domains
- MeSH terms
- Metadata, Antibodies, Clinical Trials as Topic, Humans, User-Computer Interface, Sequence Alignment, Internet, Databases, Protein
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