--- language: - en license: cc-by-4.0 license_link: LICENSE.md tags: - biology - chemistry dataset_summary: All data available on The Structural Antibody Database (SAbDab) pretty_name: Raw data from The Structural Antibody Database (SAbDab) dataset_description: This dataset contains all available data from the SAbDab as of Mar 4, 2026. The SAbDab is a database of antibody structures including experimental details, antibody nomenclature, affinity data and sequence annotations. acknowledgements: 'We kindly acknowledge the SAbDab team, RosettaCommons, and the following institutions: University of California, Los Angeles; University of Maryland; University of Oregon; University of Michigan; University of Pennsylvania; and the Wistar Institute' size_categories: - 10K- @article{10.1093/nar/gkt1043, author = {Dunbar, James and Krawczyk, Konrad and Leem, Jinwoo and Baker, Terry and Fuchs, Angelika and Georges, Guy and Shi, Jiye and Deane, Charlotte M.}, title = {SAbDab: the structural antibody database}, journal = {Nucleic Acids Research}, volume = {42}, number = {D1}, pages = {D1140-D1146}, year = {2013}, month = {11}, abstract = {Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available antibody structures annotated and presented in a consistent fashion. The data are annotated with several properties including experimental information, gene details, correct heavy and light chain pairings, antigen details and, where available, antibody–antigen binding affinity. The user can select structures, according to these attributes as well as structural properties such as complementarity determining region loop conformation and variable domain orientation. Individual structures, datasets and the complete database can be downloaded.}, issn = {0305-1048}, doi = {10.1093/nar/gkt1043}, url = {https://doi.org/10.1093/nar/gkt1043}, eprint = {https://academic.oup.com/nar/article-pdf/42/D1/D1140/3538157/gkt1043.pdf}} citation_apa: >- James Dunbar, Konrad Krawczyk, Jinwoo Leem, Terry Baker, Angelika Fuchs, Guy Georges, Jiye Shi, Charlotte M. Deane, SAbDab: the structural antibody database, Nucleic Acids Research, Volume 42, Issue D1, 1 January 2014, Pages D1140–D1146, https://doi.org/10.1093/nar/gkt1043 --- # All raw data from The Structural Antibody Database (SAbDab) ## Quickstart Usage ### Install HuggingFace Datasets package Each subset can be loaded into python using the Huggingface [datasets](https://huggingface.co/docs/datasets/index) library. First, from the command line install the `datasets` library $ pip install datasets Optionally set the cache directory, e.g. $ HF_HOME=${HOME}/.cache/huggingface/ $ export HF_HOME then, from within python load the datasets library >>> import datasets ### Load model datasets To load structures from the entire `SAbDab` dataset, use `datasets.load_dataset(...)`: >>> dataset_tag = "train" >>> dataset_models = datasets.load_dataset( path = "ProteinMPNN/SAbDab_raw", name = f"{dataset_tag}_models", data_dir = f"{dataset_tag}")['train'] and the dataset is loaded as a `datasets.arrow_dataset.Dataset` >>> dataset_models Dataset({ features: [ 'pdb', 'Hchain', 'Lchain', 'model', 'antigen_chain', 'antigen_type', 'antigen_het_name', 'antigen_name', 'short_header', 'date', 'compound', 'organism', 'heavy_species', 'light_species', 'antigen_species', 'authors', 'resolution', 'method', 'r_free', 'r_factor', 'scfv', 'engineered', 'heavy_subclass', 'light_subclass', 'light_ctype', 'affinity', 'delta_g', 'affinity_method', 'temperature', 'pmid' ], num_rows: 20701 }) which is a column oriented format that can be accessed directly, converted in to a `pandas.DataFrame`, or `parquet` format, e.g. >>> dataset_models.data.column('pdb') >>> dataset_models.to_pandas() >>> dataset_models.to_parquet("dataset.parquet") ## Dataset Details ### Dataset Description This dataset contains all available data from the SAbDab as of Mar 4, 2026. The SAbDab is a database of antibody structures including experimental details, antibody nomenclature, affinity data and sequence annotations. - **Acknowledgements:** We kindly acknowledge the SAbDab team, RosettaCommons, and the following institutions: University of California, Los Angeles; University of Maryland; University of Oregon; University of Michigan; University of Pennsylvania; and the Wistar Institute. - **License:** CC-BY 4.0 ### Dataset Sources - **Paper:** Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 ## Uses Screening of antibody-antigen interactions, querying structural features of antibodies, and more ## Citation @article{10.1093/nar/gkt1043, author = {Dunbar, James and Krawczyk, Konrad and Leem, Jinwoo and Baker, Terry and Fuchs, Angelika and Georges, Guy and Shi, Jiye and Deane, Charlotte M.}, title = {SAbDab: the structural antibody database}, journal = {Nucleic Acids Research}, volume = {42}, number = {D1}, pages = {D1140-D1146}, year = {2013}, month = {11}, abstract = {Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available antibody structures annotated and presented in a consistent fashion. The data are annotated with several properties including experimental information, gene details, correct heavy and light chain pairings, antigen details and, where available, antibody–antigen binding affinity. The user can select structures, according to these attributes as well as structural properties such as complementarity determining region loop conformation and variable domain orientation. Individual structures, datasets and the complete database can be downloaded.}, issn = {0305-1048}, doi = {10.1093/nar/gkt1043}, url = {https://doi.org/10.1093/nar/gkt1043}, eprint = {https://academic.oup.com/nar/article-pdf/42/D1/D1140/3538157/gkt1043.pdf} } ## Dataset Card Authors Miranda Simpson (miranda13nicoles@gmail.com), Becca Lee (beccalee5@g.ucla.edu), Nathaniel Felbinger (nfelbing@umd.edu), Pratyush Dhal (pdhal@umich.edu), Colby Agostino (colby.agostino@pennmedicine.upenn.edu)