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Datasets:
Bindwell
/
PLBA

Tags:
binding-affinity
biology
chemistry
License:
Dataset card Files
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The dataset viewer is not available for this dataset.
Cannot get the config names for the dataset.
Error code:   ConfigNamesError
Exception:    FileNotFoundError
Message:      Couldn't find any data file at /src/services/worker/Bindwell/PLBA. Couldn't find 'Bindwell/PLBA' on the Hugging Face Hub either: FileNotFoundError: Unable to find 'hf://datasets/Bindwell/PLBA@af381203364b0d65d4e7fe3f0a8ae1c5d26b6a41/pdbbind-2020-general-equal-only.parquet' with any supported extension ['.csv', '.tsv', '.json', '.jsonl', '.ndjson', '.parquet', '.geoparquet', '.gpq', '.arrow', '.txt', '.tar', '.xml', '.blp', '.bmp', '.dib', '.bufr', '.cur', '.pcx', '.dcx', '.dds', '.ps', '.eps', '.fit', '.fits', '.fli', '.flc', '.ftc', '.ftu', '.gbr', '.gif', '.grib', '.png', '.apng', '.jp2', '.j2k', '.jpc', '.jpf', '.jpx', '.j2c', '.icns', '.ico', '.im', '.iim', '.tif', '.tiff', '.jfif', '.jpe', '.jpg', '.jpeg', '.mpg', '.mpeg', '.msp', '.pcd', '.pxr', '.pbm', '.pgm', '.ppm', '.pnm', '.psd', '.bw', '.rgb', '.rgba', '.sgi', '.ras', '.tga', '.icb', '.vda', '.vst', '.webp', '.wmf', '.emf', '.xbm', '.xpm', '.BLP', '.BMP', '.DIB', '.BUFR', '.CUR', '.PCX', '.DCX', '.DDS', '.PS', '.EPS', '.FIT', '.FITS', '.FLI', '.FLC', '.FTC', '.FTU', '.GBR', '.GIF', '.GRIB', '.PNG', '.APNG', '.JP2', '.J2K', '.JPC', '.JPF', '.JPX', '.J2C', '.ICNS', '.ICO', '.IM', '.IIM', '.TIF', '.TIFF', '.JFIF', '.JPE', '.JPG', '.JPEG', '.MPG', '.MPEG', '.MSP', '.PCD', '.PXR', '.PBM', '.PGM', '.PPM', '.PNM', '.PSD', '.BW', '.RGB', '.RGBA', '.SGI', '.RAS', '.TGA', '.ICB', '.VDA', '.VST', '.WEBP', '.WMF', '.EMF', '.XBM', '.XPM', '.aiff', '.au', '.avr', '.caf', '.flac', '.htk', '.svx', '.mat4', '.mat5', '.mpc2k', '.ogg', '.paf', '.pvf', '.raw', '.rf64', '.sd2', '.sds', '.ircam', '.voc', '.w64', '.wav', '.nist', '.wavex', '.wve', '.xi', '.mp3', '.opus', '.3gp', '.3g2', '.avi', '.asf', '.flv', '.mp4', '.mov', '.m4v', '.mkv', '.webm', '.f4v', '.wmv', '.wma', '.ogm', '.mxf', '.nut', '.AIFF', '.AU', '.AVR', '.CAF', '.FLAC', '.HTK', '.SVX', '.MAT4', '.MAT5', '.MPC2K', '.OGG', '.PAF', '.PVF', '.RAW', '.RF64', '.SD2', '.SDS', '.IRCAM', '.VOC', '.W64', '.WAV', '.NIST', '.WAVEX', '.WVE', '.XI', '.MP3', '.OPUS', '.3GP', '.3G2', '.AVI', '.ASF', '.FLV', '.MP4', '.MOV', '.M4V', '.MKV', '.WEBM', '.F4V', '.WMV', '.WMA', '.OGM', '.MXF', '.NUT', '.pdf', '.PDF', '.zip']
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 66, in compute_config_names_response
                  config_names = get_dataset_config_names(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 161, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1027, in dataset_module_factory
                  raise FileNotFoundError(
              FileNotFoundError: Couldn't find any data file at /src/services/worker/Bindwell/PLBA. Couldn't find 'Bindwell/PLBA' on the Hugging Face Hub either: FileNotFoundError: Unable to find 'hf://datasets/Bindwell/PLBA@af381203364b0d65d4e7fe3f0a8ae1c5d26b6a41/pdbbind-2020-general-equal-only.parquet' with any supported extension ['.csv', '.tsv', '.json', '.jsonl', '.ndjson', '.parquet', '.geoparquet', '.gpq', '.arrow', '.txt', '.tar', '.xml', '.blp', '.bmp', '.dib', '.bufr', '.cur', '.pcx', '.dcx', '.dds', '.ps', '.eps', '.fit', '.fits', '.fli', '.flc', '.ftc', '.ftu', '.gbr', '.gif', '.grib', '.png', '.apng', '.jp2', '.j2k', '.jpc', '.jpf', '.jpx', '.j2c', '.icns', '.ico', '.im', '.iim', '.tif', '.tiff', '.jfif', '.jpe', '.jpg', '.jpeg', '.mpg', '.mpeg', '.msp', '.pcd', '.pxr', '.pbm', '.pgm', '.ppm', '.pnm', '.psd', '.bw', '.rgb', '.rgba', '.sgi', '.ras', '.tga', '.icb', '.vda', '.vst', '.webp', '.wmf', '.emf', '.xbm', '.xpm', '.BLP', '.BMP', '.DIB', '.BUFR', '.CUR', '.PCX', '.DCX', '.DDS', '.PS', '.EPS', '.FIT', '.FITS', '.FLI', '.FLC', '.FTC', '.FTU', '.GBR', '.GIF', '.GRIB', '.PNG', '.APNG', '.JP2', '.J2K', '.JPC', '.JPF', '.JPX', '.J2C', '.ICNS', '.ICO', '.IM', '.IIM', '.TIF', '.TIFF', '.JFIF', '.JPE', '.JPG', '.JPEG', '.MPG', '.MPEG', '.MSP', '.PCD', '.PXR', '.PBM', '.PGM', '.PPM', '.PNM', '.PSD', '.BW', '.RGB', '.RGBA', '.SGI', '.RAS', '.TGA', '.ICB', '.VDA', '.VST', '.WEBP', '.WMF', '.EMF', '.XBM', '.XPM', '.aiff', '.au', '.avr', '.caf', '.flac', '.htk', '.svx', '.mat4', '.mat5', '.mpc2k', '.ogg', '.paf', '.pvf', '.raw', '.rf64', '.sd2', '.sds', '.ircam', '.voc', '.w64', '.wav', '.nist', '.wavex', '.wve', '.xi', '.mp3', '.opus', '.3gp', '.3g2', '.avi', '.asf', '.flv', '.mp4', '.mov', '.m4v', '.mkv', '.webm', '.f4v', '.wmv', '.wma', '.ogm', '.mxf', '.nut', '.AIFF', '.AU', '.AVR', '.CAF', '.FLAC', '.HTK', '.SVX', '.MAT4', '.MAT5', '.MPC2K', '.OGG', '.PAF', '.PVF', '.RAW', '.RF64', '.SD2', '.SDS', '.IRCAM', '.VOC', '.W64', '.WAV', '.NIST', '.WAVEX', '.WVE', '.XI', '.MP3', '.OPUS', '.3GP', '.3G2', '.AVI', '.ASF', '.FLV', '.MP4', '.MOV', '.M4V', '.MKV', '.WEBM', '.F4V', '.WMV', '.WMA', '.OGM', '.MXF', '.NUT', '.pdf', '.PDF', '.zip']

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Binding Affinity Dataset

Overview

This dataset is a comprehensive collection of protein-ligand binding affinity data, compiled from multiple sources. The dataset is structured with multiple splits, each corresponding to a specific source:

  • train split (glaser.parquet)
  • val split (pdbbind-2013-core.parquet)
  • davis split
  • davis_filtered split
  • kiba split
  • pdbbind_2020_general split
  • pdbbind_2020_refined split
  • pdbbind_2013_core split
  • bindingdb_ic50 split
  • bindingdb_ki split
  • bindingdb_kd_filtered split
  • bindingdb_kd split
  • glaser split

Training Dataset Composition

The training split uses the Glaser dataset, while the validation split uses the PDBBind 2013 Core dataset.

Data Sources

Dataset Source Notes
bindingdb_ic50.parquet TDC Python Package Therapeutic Data Commons
bindingdb_kd.parquet TDC Python Package Therapeutic Data Commons
bindingdb_kd_filtered.parquet Manually Filtered See standardize_data.ipynb
bindingdb_ki.parquet TDC Python Package Therapeutic Data Commons
davis.parquet TDC Python Package Therapeutic Data Commons
davis_filtered.parquet Kaggle Dataset Filtered Davis dataset
kiba.parquet TDC Python Package Therapeutic Data Commons
pdbbind_2020_general.parquet PDBBind General PDBBind 2020 dataset
pdbbind_2020_refined.parquet PDBBind Refined PDBBind 2020 dataset
pdbbind_2013_core.parquet PDBBind Core PDBBind 2013 dataset
glaser.parquet HuggingFace Dataset Glaser binding affinity dataset

Dataset Columns

Column Description
seq Protein sequence
smiles_can Canonical SMILES representation of the ligand
affinity_uM Binding affinity in micromolar (µM) concentration
neg_log10_affinityM Negative logarithm (base 10) of the affinity in molar concentration
affinity_norm Normalized binding affinity
affinity_mean Mean binding affinity for duplicate protein-ligand pairs
affinity_std Standard deviation of binding affinity for duplicate protein-ligand pairs
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