User Guide
A step-by-step tutorial for using MCKcat to predict enzyme turnover numbers (kcat) and guide rational enzyme evolution.
Single Pair Prediction
Predict kcat for one enzyme–reaction pair at a time. Input enzyme sequence and full reaction (substrates + products).
Required Inputs
- Enzyme Sequence: Standard amino acid sequence (1–1000 residues)
- Reaction SMILES: Full reaction in SMILES format (substrates>>products)
- Alternative: Substrates and products as separate valid SMILES or InChI strings
Input Format Rules
Reaction SMILES Example:
O=C(CO)CO>>O=CC=O.O
Enzyme Sequence Example:
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Tip
Use “>>” to separate substrates and products. Use “.” to separate multiple molecules.
Batch Prediction (Multiple Pairs)
High-throughput kcat prediction for many enzyme–reaction pairs via CSV upload.
CSV Format Specification
- Three required columns:
Sequence,substrates,products - Sequence: Amino acid string (≤1000 residues)
- substrates: SMILES or InChI (multiple separated by “.”)
- products: SMILES or InChI (multiple separated by “.”)
CSV Template
| Sequence | substrates | products |
|---|---|---|
| MAKDEAI... | O=C(O)C(=O)CO | O=CC=O.O |
| MKKLLIA... | O=CC1=CC=CC=C1 | O=C(O)C1=CC=CC=C1 |
How to Use
- Download the example CSV template
- Fill in your enzyme sequences and reaction SMILES/InChI
- Upload the CSV file
- Wait for prediction (10–60 seconds depending on size)
- Download results as CSV
About Predictions
- Sequences longer than 1000 residues are automatically truncated
- Invalid residues (U, Z, B, O) are replaced with X
- Model supports wild‑type enzymes and designed mutants
- Designed for oxidoreductases, transferases, hydrolases, and lyases
Important Notes
- Ensure SMILES and InChI strings are valid
- Batch jobs are limited to 200 pairs per upload
- Predictions are for aqueous, near‑physiological conditions
- Results are for rational enzyme design, not for clinical use
- For best performance, use full‑length native sequences
Ready to Start?
Go to Single Pair or Multiple Pairs to begin your kcat prediction and enzyme engineering.
Start Predicting