README.md 542 Bytes
Newer Older
Ninjani's avatar
Ninjani committed
1
2
3
4
5
6
## Matchmaker - A joint structure-molecule framework to predict protein-compound specificity

### Dependencies
- modeller
- RDKit
- shap
Ninjani's avatar
Ninjani committed
7
8
9
- XGBoost
- APBS
- PDB2PQR
Ninjani's avatar
Ninjani committed
10
11
12
13
14
15
16
17
- geometricus
- caretta

### Code
- `modelling_functions.py` - functions to align protein sequences to templates and prepare for modelling.
- `parallel_model.py`: generate homology models in parallel
- `make_data.py`: functions for extracting features from protein sequences and homology models
- `prediction.py`: functions for training and interpreting Matchmaker classifiers.