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Published workflow · Temple Compute
BioExcel Membrane MD Analysis - GABA-gated Chloride Channel (A023K)
W-26 · Protein-Membrane MD Analysis
v112 stages3 clones0
The pipeline
Every stage picks its own compute target. Temple Compute OS resolves the dependencies between them and moves the data across each boundary.
- 01Download structure and trajectory from MDDB (A023K)
- Consumes
- download_trajectory_config, src_conda_env_yaml
- Produces
- downloaded_pdb, downloaded_xtc, downloaded_tpr
- 02Fit trajectory to membrane normal (rot+trans, gmx_image)
- Consumes
- fit_membrane_config, downloaded_pdb, downloaded_xtc, src_conda_env_yaml
- Produces
- memb_fit_xtc
- 03Fit trajectory to protein XY translation (transxy, gmx_image)
- Consumes
- fit_protein_config, downloaded_pdb, memb_fit_xtc, src_conda_env_yaml
- Produces
- memb_fit_xy_xtc
- 04Identify membrane leaflets with FATSLiM
- Consumes
- identify_leaflets_fatslim_config, downloaded_pdb, downloaded_xtc
- Produces
- leaflets_ndx
- 05Assign leaflets per frame with Lipyphilic (lpp_assign_leaflets)
- Consumes
- assign_leaflets_config, downloaded_pdb, memb_fit_xy_xtc
- Produces
- leaflets_data_csv
- 06Compute lipid z-positions for whole membrane (lpp_zpositions)
- Consumes
- compute_zpositions_config, downloaded_pdb, memb_fit_xy_xtc
- Produces
- zpositions_csv
- 07Compute lipid z-positions around protein region (lpp_zpositions)
- Consumes
- compute_zpositions_around_config, downloaded_pdb, memb_fit_xy_xtc
- Produces
- zpositions_around_csv
- 08Compute deuterium order parameters of acyl tails (gorder_aa)
- Consumes
- compute_order_parameters_config, downloaded_tpr, downloaded_xtc
- Produces
- order_csv
- 09Compute area per lipid via 2D Voronoi tessellation (fatslim_apl)
- Consumes
- compute_area_per_lipid_config, downloaded_pdb, memb_fit_xtc
- Produces
- apl_csv
- 10Compute membrane density profile along z-axis (cpptraj_density)
- Consumes
- compute_density_profile_config, downloaded_pdb, memb_fit_xy_xtc, src_conda_env_yaml
- Produces
- density_dat
- 11Compute channel pore radius profile (mda_hole)
- Consumes
- compute_pore_dimensions_config, downloaded_pdb, memb_fit_xy_xtc
- Produces
- hole_vmd, hole_profile_csv
- 12Detect lipid flip-flop events across leaflets (lpp_flip_flop)
- Consumes
- compute_flip_flop_config, downloaded_pdb, memb_fit_xy_xtc, leaflets_data_csv
- Produces
- flip_flop_csv
Run this workflow
This release is frozen and self-contained: the pipeline definition, its input files, and its plugin environment. Open it in Temple Compute OS to clone it into your own account and run it on HPC or any cloud. Temple Compute OS is in private beta, so you will need an invitation first.