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Published workflow · Temple Compute
BioExcel GoDMD - Adenylate Kinase Conformational Transition
W-20 · Protein Conformational Transitions
v18 stages0 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 origin structure 1AKE (closed state) from PDB
- Consumes
- fetch_pdb_origin_config, src_conda_env_yaml
- Produces
- origin_pdb
- 02Download target structure 4AKE (open state) from PDB
- Consumes
- fetch_pdb_target_config, src_conda_env_yaml
- Produces
- target_pdb
- 03Extract chain A from origin structure (1AKE)
- Consumes
- extract_chain_origin_config, origin_pdb, src_conda_env_yaml
- Produces
- origin_chain_pdb
- 04Extract chain A from target structure (4AKE)
- Consumes
- extract_chain_target_config, target_pdb, src_conda_env_yaml
- Produces
- target_chain_pdb
- 05Remove AP5 inhibitor from origin structure (1AKE)
- Consumes
- remove_molecules_origin_config, origin_chain_pdb, src_conda_env_yaml
- Produces
- origin_nolig_pdb
- 06Compute residue mapping between origin and target (EMBOSS water alignment)
- Consumes
- godmd_prep_config, origin_nolig_pdb, target_chain_pdb, src_conda_env_yaml
- Produces
- origin_aln, target_aln
- 07Run GoDMD conformational transition simulation (1AKE → 4AKE)
- Consumes
- godmd_run_config, origin_nolig_pdb, target_chain_pdb, origin_aln, target_aln, src_conda_env_yaml
- Produces
- godmd_trj, godmd_pdb
- 08Convert GoDMD trajectory from mdcrd to XTC format
- Consumes
- cpptraj_convert_config, godmd_pdb, godmd_trj, src_conda_env_yaml
- Produces
- godmd_trj_xtc
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.