HydraMap-based features generation
CONTENTS
Notebooks
1. Generating hydration sites by HydraMap analysis:
sh gen_wat4.sh ./data
2. Generaing HydraMap-based features, RF-score features or Extended Connectivity Interaction Features:
python calFeature.py
3. Train and test:
python train_model.py --train feature_train.csv --test feature_test.csv --model xgb --out result.txt
4. save SF model：
python train_model.py --train feature_train.csv --savemod --model xgb
5. run trained SF model:
python train_model.py --test feature_test.csv --runmod --out result.txt
Folders
data: protein & ligand structure files, experimental binding affinity file, and PDBID list file
script: scripts related to features generation and modeling
Notes:
1. Protein PDB files are assumed to contain coordinates for all heavy atoms