# Research Object Crate for CWL Protein-Membrane MD analysis tutorial

Original URL: https://workflowhub.eu/workflows/2149/ro_crate?version=1

# Protein-Membrane MD analysis tutorial using BioExcel Building Blocks (biobb) *** This tutorial aims to illustrate the process of **analyzing a membrane molecular dynamics (MD) simulation** using the **BioExcel Building Blocks library (biobb)**. The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (**GABA**), a major inhibitory neurotransmitter in the brain, which was embedded in a **DPPC membrane** in the [MemProtMD](https://memprotmd.bioch.ox.ac.uk/_ref/PDB/4cof/_sim/4cof_default_dppc/) project, which trajectory is obtained from the [**MDDB**](https://mddbr.eu/), where we can find it under the [A01M6](https://irb.mddbr.eu/#/id/A01M6/overview) accession id. *** ## Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU Horizon Europe [101093290](https://cordis.europa.eu/project/id/101093290), EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). * (c) 2015-2026 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2026 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel")

Author
  Genís Bayarri, Adam Hospital
License
  Apache-2.0

## Contents

Main Workflow: CWL Protein-Membrane MD analysis tutorial
Size: 12026 bytes
Main Workflow Diagram: workflow-2149-b4ceec3fdbeb59dff77f5503a5015f285cc75476-diagram.svg
Size: 51639 bytes
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/README.md
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/structure.pdb
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/topology.tpr
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/trajectory.xtc
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/workflow_input_descriptions.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/cpptraj_density.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/fatslim_apl.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/fatslim_membranes.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/gmx_image.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/gorder_aa.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/lpp_assign_leaflets.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/lpp_flip_flop.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/lpp_zpositions.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/cwl/biobb_adapters/mda_hole.cwl