Workflows

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52 Workflows visible to you, out of a total of 52

Stable

# Summary

This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb\_conda_kernels,
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Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Douglas Lowe

Stable

# Summary

This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.

Workflow engine is a jupyter notebook. Auxiliary libraries used are nb\_conda\_kernels, os, and plotly. Environment setup can be carried out using the environment.yml in the code
...

Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Douglas Lowe

Stable

# Summary

Jupyter Notebook containing a tutorial 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
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Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Robin Long

Stable

# Summary

Common Workflow Language example that illustrate the process of setting up a
simulation system containing a protein, step by step, using the BioExcel
Building Blocks library (biobb). The particular example used is the Lysozyme
protein (PDB code 1AKI).

# Additional Links

* [View Tutorial](http://mmb.irbbarcelona.org/biobb/workflows/tutorials/md_setup)

* [View in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/master?filepath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynb)
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Type: Common Workflow Language

Creators: None

Submitter: Robin Long

Metagenomics: taxa classification

Type: Galaxy

Creator: Milad Miladi

Submitter: Willem de Koning

Genome assembly: Unicycler-based WF for Klebsiella pneumoniae [Wick et al. Microbial genomics 2017]

Type: Galaxy

Creator: Milad Miladi

Submitter: Willem de Koning

Genome assembly: Flye-based WF for highly repetitive genomes [Schmid et al. NAR 2018]

Type: Galaxy

Creator: Milad Miladi

Submitter: Willem de Koning

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