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Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb).

Two examples are provided:

  1. One uses is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease, generating parameters for the the GROMACS package.
  2. The second example used Oseltamivir (also called Tamiflu), an antiviral drug, generating parameters for use in CNS (the computational engine used for example by *HADDOCK).

OpenBabel and ACPype packages are used to add hydrogens, energetically minimize the structure, and generate parameters with Generalized Amber Force Field (GAFF) forcefield and AM1-BCC charges.

Settings

Biobb modules used

  • biobb_io: Tools to fetch data to be consumed by the rest of the Biobb building blocks.
  • biobb_chemistry: Tools to manipulate chemical data.

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.

Conda Installation and Launch

git clone https://github.com/bioexcel/biobb_wf_ligand_parameterization.git
cd biobb_wf_ligand_parameterization
conda env create -f conda_env/environment.yml
conda activate biobb_wf_ligand_parameterization

For parametrizing a ligand for use in GROMACS launch the following notebook:

jupyter-notebook biobb_wf_ligand_parameterization/notebooks/biobb_wf_ligand_parameterization.ipynb

For parametrizing a ligand for use in CNS/HADDOCK launch the following notebook:

jupyter-notebook biobb_wf_ligand_parameterization/notebooks/biobb_wf_ligand_parameterization_CNS.ipynb

Tutorial

Click here to view tutorial in Read the Docs

Click here to execute the GROMACS parametrization tutorial in Binder

Click here to execute the CNS parametrization tutorial in Binder

Click here to open tutorial in Google Colab

Version

2024.1

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).

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