Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

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galaxy-gmx-automatic-ligand-parameterization-tutor
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Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es . Please, click here to access .

This tutorial aims to illustrate the process of ligand parameterization for a small molecule , step by step, using the BioExcel Building Blocks library (biobb) . The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

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

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.

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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/bioexcel/biobb_workflows/tree/master/biobb_wf_ligand_parameterization/galaxy
Name: galaxy-gmx-automatic-ligand-parameterization-tutor
Version: Version 3
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Copyright: Public Domain
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