CMIP tutorial using BioExcel Building Blocks (biobb)

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This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), and a MD simulation of the complex formed by the SARS-CoV-2 Receptor Binding Domain and the human Angiotensin Converting Enzyme 2 (PDB code 6VW1).

The code wrapped is the Classical Molecular Interaction Potentials (CMIP) code:

Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins. Gelpí, J.L., Kalko, S.G., Barril, X., Cirera, J., de la Cruz, X., Luque, F.J. and Orozco, M. (2001) Proteins, 45: 428-437. https://doi.org/10.1002/prot.1159

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Settings

Biobb modules used

• biobb_io: Tools to fetch biomolecular data from public databases.

• biobb_cmip: Tools to compute classical molecular interaction potentials from protein structures.

• biobb_structure_utils: Tools to modify or extract information from a PDB structure.

• biobb_chemistry: Tools to perform chemoinformatics on molecular structures.

• biobb_amber: Tools to setup and simulate atomistic MD simulations using AMBER MD package.

Auxiliary libraries used

• 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.

• simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.

Conda Installation and Launch

git clone https://github.com/bioexcel/biobb_wf_cmip.git
cd biobb_wf_cmip
conda env create -f conda_env/environment.yml
conda activate biobb_CMIP_tutorial
jupyter-notebook biobb_wf_cmip/notebooks/biobb_wf_cmip.ipynb

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Tutorial

Click here to view tutorial in Read the Docs

Click here to execute tutorial in Binder

Click here to open tutorial in Google Colab

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Version

2024.1 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 H2020 823830, EU H2020 675728).

• (c) 2015-2024 Barcelona Supercomputing Center

• (c) 2015-2024 Institute for Research in Biomedicine

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