Workflows

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575 Workflows visible to you, out of a total of 680

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb) (jupyter notebook)

Testing

Work-in-progress

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 Ibuprofen small compound (3-letter code IBP, Drugbank code DB01050), a non-steroidal anti-inflammatory drug (NSAID) derived from propionic acid and it is considered the first of the propionics.

OpenBabel and ACPype packages are used to add hydrogens, energetically minimize the structure, and generate ...

Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Douglas Lowe

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Created: 16th Jul 2020 at 16:32, Last updated: 8th Sep 2020 at 13:09

Mutation Free Energy Calculations using BioExcel Building Blocks (jupyter notebook)

Testing

Work-in-progress

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 repository. The ...

Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Douglas Lowe

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Created: 4th Sep 2020 at 16:34, Last updated: 8th Sep 2020 at 12:26

Example of setting up a simulation system

Workflow Hub Administration

Stable

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).

Type: Common Workflow Language

Creators: None

Submitter: Stian Soiland-Reyes

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Created: 17th Jun 2020 at 11:25, Last updated: 7th Sep 2020 at 10:39