abYsis: integrated antibody sequence and structure-management, analysis, and prediction
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abYsis is a web-based antibody research system that includes an integrated database of antibody sequence and structure data. The system can be interrogated in numerous ways-from simple text and sequence searches to sophisticated queries that apply 3D structural constraints. The publicly available version includes pre-analyzed sequence data from the European Molecular Biology Laboratory European Nucleotide Archive (EMBL-ENA) and Kabat as well as structure data from the Protein Data Bank. A researcher's own sequences can also be analyzed through the web interface. A defining characteristic of abYsis is that the sequences are automatically numbered with a series of popular schemes such as Kabat and Chothia and then annotated with key information such as complementarity-determining regions and potential post-translational modifications. A unique aspect of abYsis is a set of residue frequency tables for each position in an antibody, allowing "unusual residues" (those rarely seen at a particular position) to be highlighted and decisions to be made on which mutations may be acceptable. This is especially useful when comparing antibodies from different species. abYsis is useful for any researcher specializing in antibody engineering, especially those developing antibodies as drugs. abYsis is available at www.abysis.org.
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According to specific criteria, antibody structures from the PDB are listed in SAbDab, a database containing 12,367 Fv region structures as of June 2022, and abYsis.
“Similarly, according to specific criteria, antibody structures from the PDB are listed in the Structural Antibody Database (SAbDab) [13], a database containing 12 367 Fv region structures as of June 2022, and abYsis [14].”
From Computational and artificial intelligence-based methods for antibody development (2023) · cites this paper as [14]
There are some ML models that predict overall developability using antibody sequences or structures.
“In addition, there are some ML models that predict overall developability using antibody sequences or structures [14,24].”
From Computational and artificial intelligence-based methods for antibody development (2023) · cites this paper as [14]
SabDab and Abysis allow retrieval of particular structures given a query antibody sequence (SAbDab) or by using more advanced features such as canonical classes of the CDRs (Abysis).
“SabDab and Abysis allow retrieval of particular structures given a query antibody sequence (SAbDab) or by using more advanced features such as canonical classes of the CDRs (Abysis).”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [47]
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References 60 · Cited by 184
- Authors
- Swindells, M. B., Porter, C. T., Couch, M., Hurst, J., Abhinandan, K. R., Nielsen, J. H., Macindoe, G., Hetherington, J., & Martin, A. C. R.
- Affiliations
- Institute of Structural and Molecular Biology (GB)
- University College London (GB)
- Corresponding author
- Martin, Andrew C.R.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2017-02
- Volume
- 429
- Issue
- 3
- Pages
- 356-364
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2509135402
- Cited by
- 184
- References
- 60
- Citations by year
- 2026: 6 · 2025: 26 · 2024: 24 · 2023: 28 · 2022: 26 · 2021: 18 · 2020: 23 · 2019: 18 · 2018: 9 · 2017: 5 · 2016: 1
- FWCI
- 9.75
- Type
- journal article
- Language
- en
- Open access
- green
- discovery.ucl.ac.uk
- Licence
- cc-by-nc-nd
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion, cc-by-nc-nd)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/K015443/1)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- hypervariable region, post-translational modification, antibody engineering, antibody drug development, online databases
- MeSH terms
- Amino Acid Sequence, Animals, Antibodies, Humans, Protein Processing, Post-Translational, Computational Biology, Internet, Complementarity Determining Regions, Databases, Protein
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