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Published workflow · Temple Compute

BioExcel Structure Checking - 1Z83 (AK1A)

W-23 · Molecular Structure Checking

v120 stages1 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.

  1. 01Download 1Z83 structure from PDB
    Consumes
    fetch_pdb_config, src_conda_env_yaml
    Produces
    downloaded_pdb
  2. 02Run initial structure quality report
    Consumes
    downloaded_pdb, src_conda_env_yaml
    Produces
    report
  3. 03Select model 1 from multi-model structure
    Consumes
    extract_model_config, downloaded_pdb, src_conda_env_yaml
    Produces
    models_pdb
  4. 04Extract chain A from structure
    Consumes
    extract_chain_config, models_pdb, src_conda_env_yaml
    Produces
    chains_pdb
  5. 05Resolve alternative locations (keep altloc A)
    Consumes
    fix_altlocs_config, chains_pdb, src_conda_env_yaml
    Produces
    altloc_pdb
  6. 06Identify and mark disulfide bridges (CYX)
    Consumes
    altloc_pdb, src_conda_env_yaml
    Produces
    ssbonds_pdb
  7. 07Remove zinc metal ions from structure
    Consumes
    remove_molecules_metals_config, ssbonds_pdb, src_conda_env_yaml
    Produces
    metals_pdb
  8. 08Remove SO4 and AP5 ligands from structure
    Consumes
    remove_molecules_ligands_config, metals_pdb, src_conda_env_yaml
    Produces
    ligands_pdb
  9. 09Strip existing hydrogen atoms
    Consumes
    ligands_pdb, src_conda_env_yaml
    Produces
    hydrogens_pdb
  10. 10Remove crystallographic water molecules
    Consumes
    hydrogens_pdb, src_conda_env_yaml
    Produces
    water_pdb
  11. 11Fix incorrect amide group assignments (ASN/GLN)
    Consumes
    water_pdb, src_conda_env_yaml
    Produces
    amides_pdb
  12. 12Fix incorrect chirality (THR/ILE side chains)
    Consumes
    amides_pdb, src_conda_env_yaml
    Produces
    chiral_pdb
  13. 13Model missing side-chain atoms
    Consumes
    chiral_pdb, src_conda_env_yaml
    Produces
    side_chains_pdb
  14. 14Fetch canonical FASTA sequence for 1Z83
    Consumes
    canonical_fasta_config, src_conda_env_yaml
    Produces
    fasta
  15. 15Model missing backbone atoms with Modeller
    Consumes
    side_chains_pdb, fasta, src_conda_env_yaml
    Produces
    backbone_pdb
  16. 16Generate AMBER topology and coordinates (LEaP)
    Consumes
    leap_gen_top_config, backbone_pdb
    Produces
    amber_pdb, amber_top, amber_crd
  17. 17Energy minimization to relieve atomic clashes (AMBER sander)
    Consumes
    sander_mdrun_config, amber_top, amber_crd
    Produces
    trj_crd, trj_rst, trj_log
  18. 18Convert minimized AMBER restart to PDB
    Consumes
    amber_top, trj_rst
    Produces
    amber_min_pdb
  19. 19Renumber residues and restore chain IDs
    Consumes
    amber_min_pdb, src_conda_env_yaml
    Produces
    final_pdb
  20. 20Run final structure quality report
    Consumes
    final_pdb, src_conda_env_yaml
    Produces
    report_final

Run this workflow

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