Create README.md

README.md

@@ -1,3 +1,146 @@
----
-license: mit
----
+---
+license: mit
+tags:
+- enzymes
+- kinetics
+- biochemistry 
+- deep-learning
+- protein
+---
+
+# CatPred-DB: Enzyme Kinetic Parameters Database
+
+- **Paper:** [CatPred: A comprehensive framework for deep learning in vitro enzyme kinetic parameters](https://www.nature.com/articles/s41467-025-57215-9)
+- **GitHub:** https://github.com/maranasgroup/CatPred-DB
+
+### Dataset Description
+
+CatPred-DB contains the benchmark datasets introduced alongside the CatPred deep learning framework for predicting in vitro enzyme kinetic parameters. The datasets cover three key kinetic parameters:
+
+| Parameter | Description | Datapoints |
+| --- | --- | --- |
+| *k*cat | Turnover number | 23,197 |
+| *K*m | Michaelis constant | 41,174 |
+| *K*i | Inhibition constant | 11,929 |
+
+These datasets were curated to address the lack of standardized, high-quality benchmarks for enzyme kinetics prediction, with particular attention to coverage of out-of-distribution enzyme sequences.
+
+## Uses
+
+### Direct Use
+This dataset is intended for training, evaluating, and benchmarking machine learning models that predict enzyme kinetic parameters from protein sequences or structural features.
+
+### Downstream Use
+The dataset can be used to 
+
+### Out-of-Scope Use
+This dataset reflects in vitro measurements and may not generalize to in vivo conditions. It should not be used as a sole basis for clinical or industrial enzyme selection without additional experimental validation.
+
+## Dataset Structure
+
+The repository contains:
+- datasets/ – CSV files for *k*cat, *K*m, and *K*i with train/test splits
+- scripts/ – Preprocessing and utility scripts
+
+## Bias, Risks, and Limitations
+
+<!-- This section is meant to convey both technical and sociotechnical limitations. -->
+
+[More Information Needed]
+
+### Recommendations
+
+<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
+
+Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.
+
+## How to Get Started with the Model
+
+Use the code below to get started with the model.
+
+[More Information Needed]
+
+## Training Details
+
+### Training Data
+
+<!-- This should link to a Dataset Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->
+
+[More Information Needed]
+
+### Training Procedure
+
+<!-- This relates heavily to the Technical Specifications. Content here should link to that section when it is relevant to the training procedure. -->
+
+#### Preprocessing [optional]
+
+[More Information Needed]
+
+
+#### Training Hyperparameters
+
+- **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision -->
+
+
+
+
+### Results
+
+[More Information Needed]
+
+#### Summary
+
+
+
+## Model Examination [optional]
+
+<!-- Relevant interpretability work for the model goes here -->
+
+[More Information Needed]
+
+
+## Technical Specifications [optional]
+
+### Model Architecture and Objective
+
+[More Information Needed]
+
+### Compute Infrastructure
+
+[More Information Needed]
+
+#### Hardware
+
+[More Information Needed]
+
+#### Software
+
+[More Information Needed]
+
+## Citation [optional]
+
+If you use this dataset, please cite:
+
+**BibTeX:**
+```bibtex
+@article{boorla2025catpred,
+  title={CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters},
+  author={Boorla, Veda Sheersh and Maranas, Costas D.},
+  journal={Nature Communications},
+  volume={16},
+  pages={2072},
+  year={2025},
+  doi={10.1038/s41467-025-57215-9}
+}
+```
+
+**APA:**  
+Boorla, V. S., & Maranas, C. D. (2025). CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters. *Nature Communications*, 16, 2072. https://doi.org/10.1038/s41467-025-57215-9
+
+## License
+
+MIT - see [LICENSE](https://github.com/maranasgroup/CatPred-DB/blob/main/LICENSE)
+
+## Model Card Authors [optional]
+
+[More Information Needed]