README.md

---
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: float64
  - name: ph
    dtype: float64
  - name: ec
    dtype: string
  - name: taxonomy_id
    dtype: float64
  - 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: float64
  - name: ph
    dtype: float64
  - name: ec
    dtype: string
  - name: taxonomy_id
    dtype: float64
  - 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: float64
  - name: ph
    dtype: float64
  - name: ec
    dtype: string
  - name: taxonomy_id
    dtype: float64
  - 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
---