This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb). The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the brain, which was embedded in a DPPC membrane in the MemProtMD project, which trajectory is obtained from the MDDB, where we can find it under the A01M6 accession id.
- biobb_io: Tools to fetch biomolecular data from public databases.
- biobb_analysis: Tools to analyse Molecular Dynamics trajectories.
- biobb_mem: Tools for membrane analysis and manipulation.
- jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
- nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
- plotly: Python interactive graphing library integrated in Jupyter notebooks.
- anywidget: Toolset for authoring reusable web-based widgets for interactive computing environments.
git clone https://github.com/bioexcel/biobb_wf_mem.git
cd biobb_wf_mem
conda env create -f conda_env/environment.yml
conda activate biobb_wf_mem
jupyter-notebook biobb_wf_mem/notebooks/biobb_wf_mem.ipynbClick here to view tutorial in Read the Docs
Click here to execute tutorial in Binder
Click here to open tutorial in Google Colab
2025.1
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) 2015-2025 Barcelona Supercomputing Center
- (c) 2015-2025 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
