# Research Object Crate for Apache Airflow Protein-Membrane MD analysis tutorial

Original URL: https://workflowhub.eu/workflows/2152/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: Apache Airflow Protein-Membrane MD analysis tutorial
Size: 2481 bytes
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/README.md
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/cpptraj_density.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/fatslim_apl.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/fatslim_membranes.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/gmx_image.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/gorder_aa.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/lpp_assign_leaflets.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/lpp_flip_flop.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/lpp_zpositions.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/biobb_adapters/mda_hole.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step10_mda_hole.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step11_lpp_flip_flop.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step1_gmx_image1.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step2_gmx_image2.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step3_fatslim_membranes.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step4_lpp_assign_leaflets.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step5_lpp_zpositions1.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step6_lpp_zpositions2.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step7_gorder_aa.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step8_fatslim_apl.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/step9_cpptraj_density.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/structure.pdb
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/topology.tpr
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_mem/airflow/inputs/trajectory.xtc