Workflows

What is a Workflow?
80 Workflows visible to you, out of a total of 81
Stable

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)

This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib (PDB Ligand code ...

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.259.2

Stable

Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.


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 ...

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.258.2

Stable

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.


This tutorial aims to 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).


Copyright & Licensing

This software has been developed in the [MMB ...

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.279.2

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). This workflow returns a resulting protein structure and simulated 3D trajectories.

Type: Common Workflow Language

Creator: Genís Bayarri

Submitters: Robin Long, Douglas Lowe

DOI: 10.48546/workflowhub.workflow.29.3

Work-in-progress

Galaxy workflow 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). This workflow returns a resulting protein structure and simulated 3D trajectories.

Designed for running on the https://dev.usegalaxy.es Galaxy instance.

Type: Galaxy

Creators: None

Submitter: Douglas Lowe

DOI: 10.48546/workflowhub.workflow.194.1

Stable

This workflow performs the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.257.1

Work-in-progress

This is an experimental KNIME workflow of using the BioExcel building blocks to implement the Protein MD Setup tutorial for molecular dynamics with GROMACS.

Note that this workflow won't import in KNIME without the experimental KNIME nodes for BioBB - contact Adam Hospital for details.

Stable

This PyCOMPSs workflow tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.

Work-in-progress

CWL version of the md_list.py workflow for HPC. This performs a system setup and runs a molecular dynamics simulation on the structure passed to this workflow. This workflow uses the md_gather.cwl sub-workflow to gather the outputs together to return these. To work with more than one structure this workflow can be called from either the md_launch.cwl workflow, or the md_launch_mutate.cwl workflow. These use scatter for parallelising the workflow. md_launch.cwl operates on a list of individual ...

Type: Common Workflow Language

Creators: None

Submitter: Douglas Lowe

DOI: 10.48546/workflowhub.workflow.121.1

Work-in-progress

CWL version of the md_list.cwl workflow for HPC.

Type: Common Workflow Language

Creators: None

Submitter: Douglas Lowe

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