Using prepared systems from MemProtMD (http://memprotmd.bioch.ox.ac.uk/)

MemProtMD is a database of around 3500 intrinsic membrane protein structures identified in the Protein Data Bank, inserted into simulated lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations.

Newport, Thomas D. et al. The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D390–D397, https://doi.org/10.1093/nar/gky1047

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Settings

Biobb modules used

• biobb_io: Tools to fetch biomolecular data from public databases.
• biobb_md: Tools to setup and run Molecular Dynamics simulations.
• biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

Auxiliar libraries used

• nb_conda_kernels: Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
• nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
• ipywidgets: Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
• os: Python miscellaneous operating system interfaces
• plotly: Python interactive graphing library integrated in Jupyter notebooks.
• simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.

Conda Installation

git clone https://github.com/bioexcel/biobb_wf_md_setup_membrane.git
cd biobb_wf_md_setup_membrane
conda env create -f conda_env/environment.yml
conda activate biobb_MDsetup_Membrane_tutorial
jupyter-nbextension enable --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview
jupyter-notebook biobb_wf_md_setup_membrane/notebooks/Membrane-Protein-MD-Setup.ipynb

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Tutorials

Click here to view tutorials in Read the Docs

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Version

2021.2 Release

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU Horizon Europe 101093290, EU H2020 823830, EU H2020 675728).

• (c) 2015-2021 Barcelona Supercomputing Center
• (c) 2015-2021 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.