| Name | dsdp JSON |
| Version |
1.0
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| Summary | Python Wrapper for DSDP |
| upload_time | 2024-10-24 12:03:32 |
| maintainer | None |
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| author | None |
| requires_python | None |
| license | None |
| keywords |
dsdp
molecular docking
|
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# DSDP: Deep Site and Docking Pose
DSDP is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.
This package is a python wrapper for DSDP.
## Installation
Please set up the python environment by [Anaconda](https://docs.anaconda.com/anaconda/install/index.html).
Create a new environment by `DSDP.yaml` :
conda env create -f DSDP.yml
The `DSDP.yaml` looks like:
```
name: DSDP
channels:
- pytorch
- nvidia
- defaults
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
- conda-forge
dependencies:
- python=3.9.0
- pip
- pytorch==2.4.0
- pytorch-cuda==12.1
- openbabel=3.1.1
- pip:
- dsdp
- tqdm==4.66.2
- scikit-image==0.24.0
```
Activate the environment
conda activate DSDP
Now, DSDP is availabel. To check whether DSDP is successfully installed, you can run the following code:
```
DSDP test
```
## Dataset
After `DSDP test`, the files in `test_data` are the example inputs.
For each complex you want to predict, you need a directory containing the ligand and protein file. For example:
```
DSDP_dataset
└───name1
│ name1_protein.pdbqt
│ name1_ligand.pdbqt
└───name2
│ name2_protein.pdbqt
│ name2_ligand.pdbqt
...
```
Input files of DSDP are pdbqt format, which can be generated by AutoDock Tools or OpenBabel.
## Run DSDP
DSDP is an integrated docking program developed for blind docking, which can also be used for redocking task. We support pdbqt input format in DSDP. You can generate it from pdb file by AutoDock Tools.
### Blind docking
For blind docking task, run:
```
DSDP blind -i ./test_data -o ./blind_results --exhaustiveness 384 --search_depth 40 --top_n 1
```
```
usage: DSDP blind [-h] -i DATASET_PATH -o O [--site_path SITE_PATH] [--exhaustiveness EXHAUSTIVENESS] [--search_depth SEARCH_DEPTH]
[--top_n TOP_N]
optional arguments:
-h, --help show this help message and exit
-i DATASET_PATH, --dataset_path DATASET_PATH
Path to the dataset file, please put the pdbqt documents of protein and ligand to one folder
-o O, --output_path O
Output path of the results
--site_path SITE_PATH
Path to the predicted sites
--exhaustiveness EXHAUSTIVENESS
Number of sampling threads
--search_depth SEARCH_DEPTH
Number of sampling steps
--top_n TOP_N Top N results are exported
```
### Redocking
For redocking task, run:
```
DSDP redock --ligand ./test_data/1a2b/1a2b_ligand.pdbqt --protein ./test_data/1a2b/1a2b_protein.pdbqt --box_min 2.241 20.008 21.314 --box_max 24.744 35.470 38.495 --exhaustiveness 384 --search_depth 40 --top_n 1 --out ./1a2b_redock.pdbqt --log ./1a2b_redock.log
```
Note: the box information (minima and maxima along x y z axis) of redocking needs to be provided by users. The box information of this example is only suitable for 1a2b protein.
```
usage: DSDP redock [-h] --ligand LIGAND --protein PROTEIN --box_min x_min y_min z_min --box_max x_max y_max z_max
[--exhaustiveness EXHAUSTIVENESS] [--search_depth SEARCH_DEPTH] [--top_n TOP_N] [--out OUT] [--log LOG]
optional arguments:
-h, --help show this help message and exit
--ligand LIGAND File name of ligand
--protein PROTEIN File name of protein
--box_min x_min y_min z_min
x y z minima of box
--box_max x_max y_max z_max
x y z maxima of box
--exhaustiveness EXHAUSTIVENESS
Number of sampling threads, default 384
--search_depth SEARCH_DEPTH
Number of sampling steps, default 40
--top_n TOP_N Top N results are exported, default 10
--out OUT Output file name of redocking, default 'OUT.pdbqt'
--log LOG Log file name of redocking, default 'OUT.log'
```
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"description": "# DSDP: Deep Site and Docking Pose\n\nDSDP is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications. \n\nThis package is a python wrapper for DSDP.\n\n## Installation\n\nPlease set up the python environment by [Anaconda](https://docs.anaconda.com/anaconda/install/index.html). \n\nCreate a new environment by `DSDP.yaml` :\n\n conda env create -f DSDP.yml\n\nThe `DSDP.yaml` looks like:\n\n```\nname: DSDP\n\nchannels:\n - pytorch\n - nvidia\n - defaults\n - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/\n - conda-forge\n\ndependencies:\n - python=3.9.0\n - pip\n - pytorch==2.4.0\n - pytorch-cuda==12.1\n - openbabel=3.1.1\n - pip:\n - dsdp\n - tqdm==4.66.2\n - scikit-image==0.24.0\n```\n\nActivate the environment\n\n conda activate DSDP\n\nNow, DSDP is availabel. To check whether DSDP is successfully installed, you can run the following code:\n\n```\n DSDP test\n```\n\n## Dataset\n\nAfter `DSDP test`, the files in `test_data` are the example inputs.\n\nFor each complex you want to predict, you need a directory containing the ligand and protein file. For example:\n\n```\nDSDP_dataset\n\u2514\u2500\u2500\u2500name1\n \u2502 name1_protein.pdbqt\n \u2502 name1_ligand.pdbqt\n\u2514\u2500\u2500\u2500name2\n \u2502 name2_protein.pdbqt\n \u2502 name2_ligand.pdbqt\n...\n```\n\nInput files of DSDP are pdbqt format, which can be generated by AutoDock Tools or OpenBabel.\n\n## Run DSDP \n\nDSDP is an integrated docking program developed for blind docking, which can also be used for redocking task. We support pdbqt input format in DSDP. You can generate it from pdb file by AutoDock Tools.\n\n### Blind docking\n\nFor blind docking task, run:\n\n```\nDSDP blind -i ./test_data -o ./blind_results --exhaustiveness 384 --search_depth 40 --top_n 1\n```\n\n```\nusage: DSDP blind [-h] -i DATASET_PATH -o O [--site_path SITE_PATH] [--exhaustiveness EXHAUSTIVENESS] [--search_depth SEARCH_DEPTH]\n [--top_n TOP_N]\n\noptional arguments:\n -h, --help show this help message and exit\n -i DATASET_PATH, --dataset_path DATASET_PATH\n Path to the dataset file, please put the pdbqt documents of protein and ligand to one folder\n -o O, --output_path O\n Output path of the results\n --site_path SITE_PATH\n Path to the predicted sites\n --exhaustiveness EXHAUSTIVENESS\n Number of sampling threads\n --search_depth SEARCH_DEPTH\n Number of sampling steps\n --top_n TOP_N Top N results are exported\n```\n\n### Redocking\n\nFor redocking task, run:\n\n```\nDSDP redock --ligand ./test_data/1a2b/1a2b_ligand.pdbqt --protein ./test_data/1a2b/1a2b_protein.pdbqt --box_min 2.241 20.008 21.314 --box_max 24.744 35.470 38.495 --exhaustiveness 384 --search_depth 40 --top_n 1 --out ./1a2b_redock.pdbqt --log ./1a2b_redock.log\n```\n\nNote: the box information (minima and maxima along x y z axis) of redocking needs to be provided by users. The box information of this example is only suitable for 1a2b protein.\n\n```\nusage: DSDP redock [-h] --ligand LIGAND --protein PROTEIN --box_min x_min y_min z_min --box_max x_max y_max z_max\n [--exhaustiveness EXHAUSTIVENESS] [--search_depth SEARCH_DEPTH] [--top_n TOP_N] [--out OUT] [--log LOG]\n\noptional arguments:\n -h, --help show this help message and exit\n --ligand LIGAND File name of ligand\n --protein PROTEIN File name of protein\n --box_min x_min y_min z_min\n x y z minima of box\n --box_max x_max y_max z_max\n x y z maxima of box\n --exhaustiveness EXHAUSTIVENESS\n Number of sampling threads, default 384\n --search_depth SEARCH_DEPTH\n Number of sampling steps, default 40\n --top_n TOP_N Top N results are exported, default 10\n --out OUT Output file name of redocking, default 'OUT.pdbqt'\n --log LOG Log file name of redocking, default 'OUT.log'\n```\n\n\n",
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