README.md

---
license: cc-by-4.0
---
Name: CatPred: A comprehensive framework for deep learning in vitro enzyme kinetic parameters

Paper: 
Boorla, V.S., Maranas, C.D. CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters. 
Nat Commun 16, 2072 (2025). https://doi.org/10.1038/s41467-025-57215-9

tags:
  - biology
  - chemistry
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
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: float
  - name: reaction_mw_diff_perc
    dtype: float
  - name: temperature
    dtype: int
  - name: ph
    dtype: float
  - name: ec
    dtype: string
  - name: taxonomy_id
    dtype: int
  - name: log10_value
    dtype: float
  - name: reactant_smiles
    dtype: string
  - name: product_smiles
    dtype: string
  - name: log10kcat_max
    dtype: float
  - name: group
    dtype: string
  - name: pdbpath
    dtype: string
  - name: reactant_smiles_20cluster
    dtype: int
  - name: sequence_20cluster
    dtype: int
  - name: reactant_smiles_40cluster
    dtype: int
  - name: sequence_40cluster
    dtype: int
  - name: reactant_smiles_60cluster
    dtype: int
  - name: sequence_60cluster
    dtype: int
  - name: reactant_smiles_80cluster
    dtype: int
  - name: sequence_80cluster
    dtype: int
  - name: reactant_smiles_99cluster
    dtype: int
  - name: sequence_99cluster
    dtype: int
  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: float
  - name: temperature
    dtype: int
  - name: ph
    dtype: float
  - name: ec
    dtype: string
  - name: taxonomy_id
    dtype: int
  - name: log10_value
    dtype: float
  - name: log10km_mean
    dtype: float
  - name: group
    dtype: string
  - name: pdbpath
    dtype: string
  - name: substrate_smiles_20cluster
    dtype: int
  - name: sequence_20cluster
    dtype: int
  - name: substrate_smiles_40cluster
    dtype: int
  - name: sequence_40cluster
    dtype: int
  - name: substrate_smiles_60cluster
    dtype: int
  - name: sequence_60cluster
    dtype: int
  - name: substrate_smiles_80cluster
    dtype: int
  - name: sequence_80cluster
    dtype: int
  - name: substrate_smiles_99cluster
    dtype: int
  - name: sequence_99cluster
    dtype: int
  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: float
  - name: temperature
    dtype: int
  - name: ph
    dtype: float
  - name: ec
    dtype: string
  - name: taxonomy_id
    dtype: int
  - name: log10_value
    dtype: float
  - name: log10ki_mean
    dtype: float
  - name: group
    dtype: string
  - name: pdbpath
    dtype: string
  - name: substrate_smiles_20cluster
    dtype: int
  - name: sequence_20cluster
    dtype: int
  - name: substrate_smiles_40cluster
    dtype: int
  - name: sequence_40cluster
    dtype: int
  - name: substrate_smiles_60cluster
    dtype: int
  - name: sequence_60cluster
    dtype: int
  - name: substrate_smiles_80cluster
    dtype: int
  - name: sequence_80cluster
    dtype: int
  - name: substrate_smiles_99cluster
    dtype: int
  - name: sequence_99cluster
    dtype: int
  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