README.md

metadata

license: cc-by-4.0
tags:
  - chemistry
  - biology
pretty_name: >-
  CatPred A comprehensive framework for deep learning in vitro enzyme kinetic
  parameters
repo: https://github.com/maranasgroup/CatPred-DB
citation_bibtex: >-
  @article{Boorla2025,title = {CatPred: a comprehensive framework for deep
  learning in vitro enzyme kinetic parameters},volume = {16},ISSN =
  {2041-1723},url = {http://dx.doi.org/10.1038/s41467-025-57215-9},DOI =
  {10.1038/s41467-025-57215-9},number = {1},journal = {Nature
  Communications},publisher = {Springer Science and Business Media LLC},author =
  {Boorla, Veda Sheersh and Maranas, Costas D.},year = {2025},month = feb}
citation_apa: >-
  Boorla, V. S., & Maranas, C. D. (2025). CatPred: a comprehensive framework for
  deep learning in vitro enzyme kinetic parameters. Nature Communications,
  16(1), 2072. doi:10.1038/s41467-025-57215-9
configs:
  - config_name: kcat
    data_files:
      - split: train
        path: kcat/kcat_train.csv
      - split: test
        path: kcat/kcat_test.csv
      - split: val
        path: kcat/kcat_val.csv
  - config_name: ki
    data_files:
      - split: train
        path: ki/ki_train.csv
      - split: test
        path: ki/ki_test.csv
      - split: val
        path: ki/ki_val.csv
  - config_name: km
    data_files:
      - split: train
        path: km/km_train.csv
      - split: test
        path: km/km_test.csv
      - split: val
        path: km/km_val.csv
dataset_info:
  - config_name: kcat
    features:
      - name: sequence
        dtype: string
      - name: sequence_source
        dtype: string
      - name: uniprot
        dtype: string
      - name: reaction_smiles
        dtype: string
      - name: value
        dtype: float64
      - name: reaction_mw_diff_perc
        dtype: float64
      - name: temperature
        dtype: int64
      - name: ph
        dtype: float64
      - name: ec
        dtype: string
      - name: taxonomy_id
        dtype: int64
      - name: log10_value
        dtype: float64
      - name: reactant_smiles
        dtype: string
      - name: product_smiles
        dtype: string
      - name: log10kcat_max
        dtype: float64
      - name: group
        dtype: string
      - name: pdbpath
        dtype: string
      - name: reactant_smiles_20cluster
        dtype: int64
      - name: sequence_20cluster
        dtype: int64
      - name: reactant_smiles_40cluster
        dtype: int64
      - name: sequence_40cluster
        dtype: int64
      - name: reactant_smiles_60cluster
        dtype: int64
      - name: sequence_60cluster
        dtype: int64
      - name: reactant_smiles_80cluster
        dtype: int64
      - name: sequence_80cluster
        dtype: int64
      - name: reactant_smiles_99cluster
        dtype: int64
      - name: sequence_99cluster
        dtype: int64
    splits:
      - name: train
        num_bytes: 28336048
        num_examples: 18750
      - name: test
        num_bytes: 3518955
        num_examples: 2315
      - name: val
        num_bytes: 3125504
        num_examples: 2083
  - config_name: km
    features:
      - name: sequence
        dtype: string
      - name: sequence_source
        dtype: string
      - name: uniprot
        dtype: string
      - name: substrate_smiles
        dtype: string
      - name: value
        dtype: float64
      - name: temperature
        dtype: int64
      - name: ph
        dtype: float64
      - name: ec
        dtype: string
      - name: taxonomy_id
        dtype: int64
      - name: log10_value
        dtype: float64
      - name: log10km_mean
        dtype: float64
      - name: group
        dtype: string
      - name: pdbpath
        dtype: string
      - name: substrate_smiles_20cluster
        dtype: int64
      - name: sequence_20cluster
        dtype: int64
      - name: substrate_smiles_40cluster
        dtype: int64
      - name: sequence_40cluster
        dtype: int64
      - name: substrate_smiles_60cluster
        dtype: int64
      - name: sequence_60cluster
        dtype: int64
      - name: substrate_smiles_80cluster
        dtype: int64
      - name: sequence_80cluster
        dtype: int64
      - name: substrate_smiles_99cluster
        dtype: int64
      - name: sequence_99cluster
        dtype: int64
    splits:
      - name: train
        num_bytes: 39599382
        num_examples: 33349
      - name: test
        num_bytes: 4847070
        num_examples: 4117
      - name: val
        num_bytes: 4405799
        num_examples: 3705
  - config_name: ki
    features:
      - name: sequence
        dtype: string
      - name: sequence_source
        dtype: string
      - name: uniprot
        dtype: string
      - name: substrate_smiles
        dtype: string
      - name: value
        dtype: float64
      - name: temperature
        dtype: int64
      - name: ph
        dtype: float64
      - name: ec
        dtype: string
      - name: taxonomy_id
        dtype: int64
      - name: log10_value
        dtype: float64
      - name: log10ki_mean
        dtype: float64
      - name: group
        dtype: string
      - name: pdbpath
        dtype: string
      - name: substrate_smiles_20cluster
        dtype: int64
      - name: sequence_20cluster
        dtype: int64
      - name: substrate_smiles_40cluster
        dtype: int64
      - name: sequence_40cluster
        dtype: int64
      - name: substrate_smiles_60cluster
        dtype: int64
      - name: sequence_60cluster
        dtype: int64
      - name: substrate_smiles_80cluster
        dtype: int64
      - name: sequence_80cluster
        dtype: int64
      - name: substrate_smiles_99cluster
        dtype: int64
      - name: sequence_99cluster
        dtype: int64
      - name: canonical_smiles
        dtype: string
    splits:
      - name: train
        num_bytes: 11601551
        num_examples: 9661
      - name: test
        num_bytes: 1429525
        num_examples: 4117
      - name: val
        num_bytes: 1291111
        num_examples: 3705