- Anaconda (v2022.10)
sudo apt install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
wget https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh
./Anaconda3-2022.10-Linux-x86_64.sh- Python 3 (v3.9.0)
conda create -n jupyter python==3.9.6 notebook
conda activate jupyter
ipython kernel install --name jupyter --user- PyMOL (v2.5.0)
conda install -c conda-forge pymol-open-source-
toml (v0.10.2): a Python library for parsing and creating TOML;
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KVFinderMD (v0.2.1): a Python package for identifying and describing cavities throughout molecular dynamics simulations;
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matplotlib (v3.6.1): a comprehensive library for creating static, animated, and interactive visualizations in Python;
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MDAnalysis (v2.3.0):a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials;
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SERD (v0.1.2): a Python package to detect solvent-exposed residues of a target biomolecule;
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nglview (v3.0.3): an IPython/Jupyter widget to interactively view molecular structures and trajectories.
pip install -r requirements.txt-
HIV-1 protease (HIV-analysis.ipynb): explore cavity alignment (grid, distance matrix and contact matrix) to group cavities throughtout the molecular dynamics trajectory;
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ALDH 1/2 (ALDH-analysis.ipynb): explore the difference of the substrate binding site volume between ALDH1 and ALDH2.
- Dataset available in: 10.5281/zenodo.7278064
The software is licensed under the terms of the MIT License and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the MIT License for more details.