RNACavityMiner: Classifiers to Mine For Ligandable Binding Cavity in RNA
git clone https://github.com/atfrank/RNACavityMiner.git
cd RNACavityMiner/
conda create -n cavityminer python=3.10
conda activate cavityminer
conda install -c conda-forge -c schrodinger pymol-bundle openbabel pandas tqdm pip pyarrow
pip3 install scikit-learn xgboost joblib
git clone https://github.com/atfrank/RNAPosers.git
cd RNAPosers/
make clean
make
cd ..
cp RNAPosers/bin/featurize bin/
rm -rf RNAPosers
Main script is src/miner_grid.sh. It requires a pdb file containing RNA 3D structure as input.
Example:
conda activate cavityminer
export CAVITYMINER="/path/to/RNACavityMiner/"
cd test/
./../src/miner_grid.sh 1ANR_1.pdb
The predicted cavities and their corresponding scores are written in file receptor/predicted_cavities.txt.
pdb tag cavityID x y z pred_MLP pred_XGB pred_RF pred_LR pred_Extra
1ANR_1 none 1 3.74 1.254 0.801000 4.322632e-02 0.106187 0.460681 3.785127e-01 0.555957
1ANR_1 none 2 3.74 1.254 12.801000 1.347721e-04 0.010728 0.250420 6.755266e-02 0.321917
1ANR_1 none 3 3.74 1.254 14.801000 1.475043e-04 0.022874 0.121178 1.792128e-02 0.225286
1ANR_1 none 4 3.74 1.254 16.800999 1.469739e-02 0.011660 0.088704 1.346384e-02 0.158415
1ANR_1 none 5 5.74 1.254 -9.199000 1.133171e-03 0.015931 0.071120 2.053839e-02 0.089329
... ... ... ... ... ... ... ... ... ... ...
1ANR_1 none 1766 -18.26 -2.746 -7.199000 2.709290e-03 0.003831 0.070224 1.418785e-02 0.088595
1ANR_1 none 1767 -18.26 -0.746 14.801000 7.025161e-09 0.003085 0.105943 2.861976e-09 0.171420
1ANR_1 none 1768 -22.26 1.254 6.801000 1.536864e-03 0.004555 0.076359 4.109725e-02 0.125883
1ANR_1 none 1769 3.74 1.254 -1.199000 1.534997e-01 0.118597 0.289568 3.087298e-01 0.392483
1ANR_1 none 1770 -12.26 -16.746 -5.199000 1.741724e-01 0.009482 0.088870 2.845870e-02 0.107240
- Jingru Xie, and Aaron T. Frank. "Mining For Ligandable Cavities in RNA" (https://doi.org/10.1021/acsmedchemlett.1c00068)
