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 execute tutorial in Binder
2026.1 Release
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) 2015-2026 Barcelona Supercomputing Center
- (c) 2015-2026 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
