All published workflows

Published workflow · Temple Compute

BioExcel HADDOCK Antibody-Antigen Protein-Protein Docking

W-24 · HADDOCK3 Protein-Protein Docking

v180 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 antibody structure 4G6K from PDB
    Consumes
    fetch_antibody_config, src_conda_env_yaml
    Produces
    ab_0_pdb
  2. 02Download antigen structure 4I1B from PDB
    Consumes
    fetch_antigen_config, src_conda_env_yaml
    Produces
    ag_0_pdb
  3. 03Download reference complex structure 4G6M from PDB
    Consumes
    fetch_complex_config, src_conda_env_yaml
    Produces
    cx_0_pdb
  4. 04Tidy antibody PDB (strict, pre H-chain extraction)
    Consumes
    ab_H_tidy_config, ab_H_tidy_in, src_conda_env_yaml
    Produces
    ab_H_tidy_out
  5. 05Extract heavy chain H from antibody
    Consumes
    ab_H_selchain_config, ab_H_selchain_in, src_conda_env_yaml
    Produces
    ab_H_selchain_out
  6. 06Remove HETATM records from antibody H chain
    Consumes
    ab_H_delhetatm_in, src_conda_env_yaml
    Produces
    ab_H_delhetatm_out
  7. 07Fix insertion codes in antibody H chain
    Consumes
    ab_H_fixinsert_in, src_conda_env_yaml
    Produces
    ab_H_fixinsert_out
  8. 08Select highest-occupancy alt-locs in antibody H chain
    Consumes
    ab_H_selaltloc_in, src_conda_env_yaml
    Produces
    ab_H_selaltloc_out
  9. 09Remove non-coordinate records from antibody H chain
    Consumes
    ab_H_keepcoord_in, src_conda_env_yaml
    Produces
    ab_H_keepcoord_out
  10. 10Select VH domain residues 1-120 from antibody H chain
    Consumes
    ab_H_selres_config, ab_H_selres_in, src_conda_env_yaml
    Produces
    ab_H_selres_out
  11. 11Final tidy of antibody H-chain reduced structure
    Consumes
    ab_H_tidy_final_in, src_conda_env_yaml
    Produces
    ab_H_reduced
  12. 12Tidy antibody PDB (strict, pre L-chain extraction)
    Consumes
    ab_L_tidy_config, ab_L_tidy_in, src_conda_env_yaml
    Produces
    ab_L_tidy_out
  13. 13Extract light chain L from antibody
    Consumes
    ab_L_selchain_config, ab_L_selchain_in, src_conda_env_yaml
    Produces
    ab_L_selchain_out
  14. 14Remove HETATM records from antibody L chain
    Consumes
    ab_L_delhetatm_in, src_conda_env_yaml
    Produces
    ab_L_delhetatm_out
  15. 15Fix insertion codes in antibody L chain
    Consumes
    ab_L_fixinsert_in, src_conda_env_yaml
    Produces
    ab_L_fixinsert_out
  16. 16Select highest-occupancy alt-locs in antibody L chain
    Consumes
    ab_L_selaltloc_in, src_conda_env_yaml
    Produces
    ab_L_selaltloc_out
  17. 17Remove non-coordinate records from antibody L chain
    Consumes
    ab_L_keepcoord_in, src_conda_env_yaml
    Produces
    ab_L_keepcoord_out
  18. 18Select VL domain residues 1-107 from antibody L chain
    Consumes
    ab_L_selres_config, ab_L_selres_in, src_conda_env_yaml
    Produces
    ab_L_selres_out
  19. 19Final tidy of antibody L-chain reduced structure
    Consumes
    ab_L_tidy_final_in, src_conda_env_yaml
    Produces
    ab_L_reduced
  20. 20Zip antibody H and L chain PDBs for merge
    Consumes
    ab_H_reduced, ab_L_reduced, src_conda_env_yaml
    Produces
    ab_HL_zip
  21. 21Merge antibody H and L chains into single PDB
    Consumes
    ab_HL_zip, src_conda_env_yaml
    Produces
    ab_clean_merge
  22. 22Renumber antibody residues starting from 1
    Consumes
    ab_reres_config, ab_reres_in, src_conda_env_yaml
    Produces
    ab_reres_out
  23. 23Set antibody chain identifier to A
    Consumes
    ab_chain_config, ab_chain_in, src_conda_env_yaml
    Produces
    ab_chain_out
  24. 24Swap segment identifier for chain identifier in antibody
    Consumes
    ab_chainxseg_in, src_conda_env_yaml
    Produces
    ab_chainxseg_out
  25. 25Final strict tidy of prepared antibody structure
    Consumes
    ab_tidy_final_config, ab_tidy_final_in, src_conda_env_yaml
    Produces
    antibody_prep
  26. 26Tidy antigen PDB (strict)
    Consumes
    ag_tidy_config, ag_tidy_in, src_conda_env_yaml
    Produces
    ag_tidy_out
  27. 27Remove HETATM records from antigen
    Consumes
    ag_delhetatm_in, src_conda_env_yaml
    Produces
    ag_delhetatm_out
  28. 28Select highest-occupancy alt-locs in antigen
    Consumes
    ag_selaltloc_in, src_conda_env_yaml
    Produces
    ag_selaltloc_out
  29. 29Remove non-coordinate records from antigen
    Consumes
    ag_keepcoord_in, src_conda_env_yaml
    Produces
    ag_keepcoord_out
  30. 30Set antigen chain identifier to B
    Consumes
    ag_chain_config, ag_chain_in, src_conda_env_yaml
    Produces
    ag_chain_out
  31. 31Swap segment identifier for chain identifier in antigen
    Consumes
    ag_chainxseg_in, src_conda_env_yaml
    Produces
    ag_chainxseg_out
  32. 32Final strict tidy of prepared antigen structure
    Consumes
    ag_tidy_final_config, ag_tidy_final_in, src_conda_env_yaml
    Produces
    antigen_prep
  33. 33Extract heavy chain H from reference complex
    Consumes
    cx_H_selchain_config, cx_H_selchain_in, src_conda_env_yaml
    Produces
    cx_H_selchain_out
  34. 34Remove HETATM from reference complex H chain
    Consumes
    cx_H_delhetatm_in, src_conda_env_yaml
    Produces
    cx_H_delhetatm_out
  35. 35Fix insertion codes in reference complex H chain
    Consumes
    cx_H_fixinsert_in, src_conda_env_yaml
    Produces
    cx_H_fixinsert_out
  36. 36Select alt-locs in reference complex H chain
    Consumes
    cx_H_selaltloc_in, src_conda_env_yaml
    Produces
    cx_H_selaltloc_out
  37. 37Keep coordinates only in reference complex H chain
    Consumes
    cx_H_keepcoord_in, src_conda_env_yaml
    Produces
    cx_H_keepcoord_out
  38. 38Select VH domain residues 1-120 from reference complex H chain
    Consumes
    cx_H_selres_config, cx_H_selres_in, src_conda_env_yaml
    Produces
    cx_H_selres_out
  39. 39Final tidy of reference complex H-chain reduced structure
    Consumes
    cx_H_tidy_final_in, src_conda_env_yaml
    Produces
    cx_H_reduced
  40. 40Extract light chain L from reference complex
    Consumes
    cx_L_selchain_config, cx_L_selchain_in, src_conda_env_yaml
    Produces
    cx_L_selchain_out
  41. 41Remove HETATM from reference complex L chain
    Consumes
    cx_L_delhetatm_in, src_conda_env_yaml
    Produces
    cx_L_delhetatm_out
  42. 42Fix insertion codes in reference complex L chain
    Consumes
    cx_L_fixinsert_in, src_conda_env_yaml
    Produces
    cx_L_fixinsert_out
  43. 43Select alt-locs in reference complex L chain
    Consumes
    cx_L_selaltloc_in, src_conda_env_yaml
    Produces
    cx_L_selaltloc_out
  44. 44Keep coordinates only in reference complex L chain
    Consumes
    cx_L_keepcoord_in, src_conda_env_yaml
    Produces
    cx_L_keepcoord_out
  45. 45Select VL domain residues 1-107 from reference complex L chain
    Consumes
    cx_L_selres_config, cx_L_selres_in, src_conda_env_yaml
    Produces
    cx_L_selres_out
  46. 46Final tidy of reference complex L-chain reduced structure
    Consumes
    cx_L_tidy_final_in, src_conda_env_yaml
    Produces
    cx_L_reduced
  47. 47Zip reference complex H and L chain PDBs for merge
    Consumes
    cx_H_reduced, cx_L_reduced, src_conda_env_yaml
    Produces
    cx_HL_zip
  48. 48Merge reference complex H and L chains
    Consumes
    cx_HL_zip, src_conda_env_yaml
    Produces
    cx_ab_clean_merge
  49. 49Renumber reference complex antibody residues from 1
    Consumes
    cx_ab_reres_config, cx_ab_reres_in, src_conda_env_yaml
    Produces
    cx_ab_reres_out
  50. 50Set reference complex antibody chain to A
    Consumes
    cx_ab_chain_config, cx_ab_chain_in, src_conda_env_yaml
    Produces
    cx_ab_chain_out
  51. 51Swap segment for chain identifier in reference complex antibody
    Consumes
    cx_ab_chainxseg_in, src_conda_env_yaml
    Produces
    cx_ab_chainxseg_out
  52. 52Final strict tidy of reference complex antibody
    Consumes
    cx_ab_tidy_final_config, cx_ab_tidy_final_in, src_conda_env_yaml
    Produces
    cx_antibody_final
  53. 53Tidy reference complex PDB for antigen extraction (strict)
    Consumes
    cx_ag_tidy_config, cx_ag_tidy_in, src_conda_env_yaml
    Produces
    cx_ag_tidy_out
  54. 54Extract chain A (antigen) from reference complex
    Consumes
    cx_ag_selchain_config, cx_ag_selchain_in, src_conda_env_yaml
    Produces
    cx_ag_selchain_out
  55. 55Rename reference antigen chain to B
    Consumes
    cx_ag_chain_config, cx_ag_chain_in, src_conda_env_yaml
    Produces
    cx_ag_chain_out
  56. 56Swap segment for chain identifier in reference complex antigen
    Consumes
    cx_ag_chainxseg_in, src_conda_env_yaml
    Produces
    cx_ag_chainxseg_out
  57. 57Remove HETATM from reference complex antigen
    Consumes
    cx_ag_delhetatm_in, src_conda_env_yaml
    Produces
    cx_ag_delhetatm_out
  58. 58Fix insertion codes in reference complex antigen
    Consumes
    cx_ag_fixinsert_in, src_conda_env_yaml
    Produces
    cx_ag_fixinsert_out
  59. 59Select alt-locs in reference complex antigen
    Consumes
    cx_ag_selaltloc_in, src_conda_env_yaml
    Produces
    cx_ag_selaltloc_out
  60. 60Keep coordinates only in reference complex antigen
    Consumes
    cx_ag_keepcoord_in, src_conda_env_yaml
    Produces
    cx_ag_keepcoord_out
  61. 61Final strict tidy of reference complex antigen
    Consumes
    cx_ag_tidy_final_config, cx_ag_tidy_final_in, src_conda_env_yaml
    Produces
    cx_antigen_final
  62. 62Zip reference complex antibody and antigen PDBs for merge
    Consumes
    cx_antibody_final, cx_antigen_final, src_conda_env_yaml
    Produces
    cx_HL_B_zip
  63. 63Merge reference complex antibody and antigen chains
    Consumes
    cx_HL_B_zip, src_conda_env_yaml
    Produces
    cx_clean_merge
  64. 64Final strict tidy of reference complex structure
    Consumes
    cx_tidy_final_config, cx_tidy_final_in, src_conda_env_yaml
    Produces
    complex_prep
  65. 65Write antibody paratope active residues file
    Consumes
    src_conda_env_yaml
    Produces
    ab_actpass
  66. 66Compute passive residues around antigen epitope
    Consumes
    passive_from_active_config, antigen_prep, src_conda_env_yaml
    Produces
    ag_actpass
  67. 67Convert active/passive residues to ambiguous restraints (AIR)
    Consumes
    actpass_to_ambig_config, ab_actpass, ag_actpass, src_conda_env_yaml
    Produces
    complex_tbl
  68. 68Generate multi-body restraints to tie antibody chains
    Consumes
    antibody_prep, src_conda_env_yaml
    Produces
    body_tbl
  69. 69Build HADDOCK topology for both molecules
    Consumes
    antibody_prep, antigen_prep, src_conda_env_yaml
    Produces
    mol1_top_zip, mol2_top_zip, haddock_wf_data
  70. 70Rigid-body docking (rigidbody, 10 models)
    Consumes
    rigid_body_config, haddock_wf_data_in, complex_tbl, body_tbl, src_conda_env_yaml
    Produces
    haddock_wf_data_rigid, docking_zip
  71. 71CAPRI evaluation after rigid-body docking
    Consumes
    haddock_wf_data_in, complex_prep, src_conda_env_yaml
    Produces
    haddock_wf_data_capri1, caprieval1_zip
  72. 72Select top-8 scoring rigid-body models
    Consumes
    sele_top_config, haddock_wf_data_in, src_conda_env_yaml
    Produces
    haddock_wf_data_sele, selection_zip
  73. 73Flexible refinement of selected models
    Consumes
    flex_ref_config, haddock_wf_data_in, complex_tbl, body_tbl, src_conda_env_yaml
    Produces
    haddock_wf_data_flex, flexref_zip
  74. 74CAPRI evaluation after flexible refinement
    Consumes
    haddock_wf_data_in, complex_prep, src_conda_env_yaml
    Produces
    haddock_wf_data_capri2, caprieval2_zip
  75. 75Energy minimisation refinement of selected models
    Consumes
    em_ref_config, haddock_wf_data_in, complex_tbl, body_tbl, src_conda_env_yaml
    Produces
    haddock_wf_data_em, emref_zip
  76. 76CAPRI evaluation after energy minimisation
    Consumes
    haddock_wf_data_in, complex_prep, src_conda_env_yaml
    Produces
    haddock_wf_data_capri3, caprieval3_zip
  77. 77Cluster refined models by FCC
    Consumes
    clust_fcc_config, haddock_wf_data_in, src_conda_env_yaml
    Produces
    haddock_wf_data_clust, clustfcc_zip
  78. 78Select top 4 models from each cluster
    Consumes
    sele_top_clusts_config, haddock_wf_data_in, src_conda_env_yaml
    Produces
    haddock_wf_data_seletop, seletopclusts_zip
  79. 79Final CAPRI evaluation on cluster representatives
    Consumes
    haddock_wf_data_in, complex_prep, src_conda_env_yaml
    Produces
    haddock_wf_data_capri4, caprieval4_zip
  80. 80Generate contact maps for cluster representatives
    Consumes
    haddock_wf_data_in, src_conda_env_yaml
    Produces
    haddock_wf_data_contact, contactmap_zip

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.

Run this in Temple Compute OSRequest an invitation