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项目作者： atfrank

项目描述 ：
Classifiers to Mine For Ligandable Binding Cavity in RNA
高级语言： Shell
项目地址: git://github.com/atfrank/RNACavityMiner.git
创建时间： 2020-08-18T06:00:04Z
项目社区：https://github.com/atfrank/RNACavityMiner
开源协议：Other
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RNACavityMiner

RNACavityMiner: Classifiers to Mine For Ligandable Binding Cavity in RNA

Download RNACavityMiner

  1. git clone https://github.com/atfrank/RNACavityMiner.git
  2. cd RNACavityMiner/

Install Dependencies

Python Modules

  1. conda create -n cavityminer python=3.10
  2. conda activate cavityminer
  3. conda install -c conda-forge -c schrodinger pymol-bundle openbabel pandas tqdm pip pyarrow
  4. pip3 install scikit-learn xgboost joblib

RNAPosers

  1. git clone https://github.com/atfrank/RNAPosers.git
  2. cd RNAPosers/
  3. make clean
  4. make
  5. cd ..
  6. cp RNAPosers/bin/featurize bin/
  7. rm -rf RNAPosers

Using RNACavityMiner

Main script is src/miner_grid.sh. It requires a pdb file containing RNA 3D structure as input.
Example:

  1. conda activate cavityminer
  2. export CAVITYMINER="/path/to/RNACavityMiner/"
  3. cd test/
  4. ./../src/miner_grid.sh 1ANR_1.pdb

The predicted cavities and their corresponding scores are written in file receptor/predicted_cavities.txt.

Output

  1. pdb     tag   cavityID      x       y          z      pred_MLP  pred_XGB   pred_RF       pred_LR  pred_Extra                                                                                                      
  2. 1ANR_1  none         1   3.74   1.254   0.801000  4.322632e-02  0.106187  0.460681  3.785127e-01    0.555957
  3. 1ANR_1  none         2   3.74   1.254  12.801000  1.347721e-04  0.010728  0.250420  6.755266e-02    0.321917
  4. 1ANR_1  none         3   3.74   1.254  14.801000  1.475043e-04  0.022874  0.121178  1.792128e-02    0.225286
  5. 1ANR_1  none         4   3.74   1.254  16.800999  1.469739e-02  0.011660  0.088704  1.346384e-02    0.158415
  6. 1ANR_1  none         5   5.74   1.254  -9.199000  1.133171e-03  0.015931  0.071120  2.053839e-02    0.089329
  7. ...      ...       ...    ...     ...        ...           ...       ...       ...           ...         ...
  8. 1ANR_1  none      1766 -18.26  -2.746  -7.199000  2.709290e-03  0.003831  0.070224  1.418785e-02    0.088595
  9. 1ANR_1  none      1767 -18.26  -0.746  14.801000  7.025161e-09  0.003085  0.105943  2.861976e-09    0.171420
  10. 1ANR_1  none      1768 -22.26   1.254   6.801000  1.536864e-03  0.004555  0.076359  4.109725e-02    0.125883
  11. 1ANR_1  none      1769   3.74   1.254  -1.199000  1.534997e-01  0.118597  0.289568  3.087298e-01    0.392483
  12. 1ANR_1  none      1770 -12.26 -16.746  -5.199000  1.741724e-01  0.009482  0.088870  2.845870e-02    0.107240

Publications

Data and ML-Code

  • DOI