Initial upload

.gitattributes

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 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+*.csv filter=lfs diff=lfs merge=lfs -text
+*.tsv filter=lfs diff=lfs merge=lfs -text
+*.pdb filter=lfs diff=lfs merge=lfs -text
+*.cif filter=lfs diff=lfs merge=lfs -text

README.md

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----
-license: cc-by-4.0
----
+---
+license: cc-by-4.0
+language  en
+tags:
+ - Biology,
+ - Antibody,
+ - RosettaCommons,
+pretty_name: Antibody dataset
+repo:
+dataset_summary: >-
+
+citation_bibtex: |-
+ @article{Huang2025,
+   title = {SAAINT-DB: a comprehensive structural antibody database for antibody modeling and design},
+   volume = {46},
+   ISSN = {1745-7254},
+   url = {http://dx.doi.org/10.1038/s41401-025-01608-5},
+   DOI = {10.1038/s41401-025-01608-5},
+   number = {12},
+   journal = {Acta Pharmacologica Sinica},
+   publisher = {Springer Science and Business Media LLC},
+   author = {Huang,  Xiaoqiang and Zhou,  Jun and Chen,  Shuang and Xia,  Xiaofeng and Chen,  Y. Eugene and Xu,  Jie},
+   year = {2025},
+   month = jun,
+   pages = {3365–3375}
+ }
+
+---
+
+# SAAINTDB
+ 
+
+## Dataset Splits
+The dataset was split at the PDB level into train, validation, and test sets (70/15/15). 
+To maintain balanced distributions, the split was stratified based on the HL label (heavy/light chain availability).
+To prevent data leakage, all entries originating from the same PDB ID were assigned to the same split.
+
+The resulting splits are provided as CSV files in the `data/` directory.
+The corresponding PDB structures for each split are also provided in the `PDB/` directory.
+
+- train.csv rows: 15033 | number of unique PDB_ID in train split: 7649
+- validation.csv rows: 3179 | number of unique PDB_ID in validation split: 1639
+- test.csv rows: 3188 | number of unique PDB_ID in test split: 1639
+
+
+## Dataset Processing
+The following preprocessing steps were performed to construct the dataset:
+1. Added a `PDB_ID_chain` column to serve as a unique identifier for each antibody entry (PDB ID + chain)
+
+2. Added an `hl_label` column indicating chain availability:
+  - `HL`: both heavy and light chains present
+  - `H_only`: only heavy chain present
+  - `L_only`: only light chain present  
+  This label was later used for balanced dataset splitting.
+
+3. Some PDB entries referenced in the dataset were missing structure files.  
+We identified the missing entries and downloaded 111 mmCIF files from the RCSB Protein Data Bank (PDB),
+updating the dataset to reflect the available structures as of February 2026.
+
+4. FASTA files corresponding to the downloaded CIF structures were missing and were subsequently generated/added.
+
+5. The dataset was split into **train, validation, and test sets (70/15/15)**.  
+
+6. A `split` column was added to the dataset to indicate the assigned subset (`train`, `validation`, or `test`).
+
+7. The processed dataset is organized as follows:
+  - `data/` : contains three CSV files (`train.csv`, `validation.csv`, `test.csv`)
+  - `PDB/` : contains PDB structure files organized into `train/`, `validation/`, and `test/` directories
+
+8. For reproducibility, the file `saaintdb_raw_data_20260226.csv` corresponds to the original dataset file `saaintdb_20260226_all.tsv`, 
+which was downloaded from the official SAAINTDB GitHub repository and converted to CSV format for easier processing.
+
+
+## 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
+
+then, from within python load the datasets library
+
+    >>> import datasets
+
+
+### Load dataset
+Load the 'RosettaCommons/SAAINTDB' dataset.
+
+ 
+## Citation
+ @article{Huang2025,
+   title = {SAAINT-DB: a comprehensive structural antibody database for antibody modeling and design},
+   volume = {46},
+   ISSN = {1745-7254},
+   url = {http://dx.doi.org/10.1038/s41401-025-01608-5},
+   DOI = {10.1038/s41401-025-01608-5},
+   number = {12},
+   journal = {Acta Pharmacologica Sinica},
+   publisher = {Springer Science and Business Media LLC},
+   author = {Huang,  Xiaoqiang and Zhou,  Jun and Chen,  Shuang and Xia,  Xiaofeng and Chen,  Y. Eugene and Xu,  Jie},
+   year = {2025},
+   month = jun,
+   pages = {3365–3375}
+ }

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