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BioExcel FlexServ - Protein Conformational Dynamics (1A32)

W-21 · Macromolecular Coarse-Grained Flexibility

v148 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 1A32 structure from PDB
    Consumes
    fetch_pdb_config
    Produces
    downloaded_pdb
  2. 02Extract C-alpha atoms from structure
    Consumes
    extract_atoms_ca_config, downloaded_pdb
    Produces
    ca_pdb
  3. 03Run Brownian Dynamics (BD) conformational ensemble
    Consumes
    bd_run_config, ca_pdb
    Produces
    bd_crd, bd_log
  4. 04Compute RMSD for BD ensemble trajectory
    Consumes
    cpptraj_rms_bd_config, ca_pdb, bd_crd
    Produces
    bd_rmsd, bd_xtc
  5. 05Run Discrete Molecular Dynamics (DMD) conformational ensemble
    Consumes
    ca_pdb
    Produces
    dmd_crd, dmd_log
  6. 06Compute RMSD for DMD ensemble trajectory
    Consumes
    cpptraj_rms_dmd_config, ca_pdb, dmd_crd
    Produces
    dmd_rmsd, dmd_xtc
  7. 07Run Normal Mode Analysis (NMA) conformational ensemble
    Consumes
    nma_run_config, ca_pdb
    Produces
    nma_crd, nma_log
  8. 08Compute RMSD for NMA ensemble trajectory
    Consumes
    cpptraj_rms_nma_config, ca_pdb, nma_crd
    Produces
    nma_rmsd, nma_xtc
  9. 09Compress BD trajectory with PCA (PCZ format)
    Consumes
    pcz_zip_bd_config, ca_pdb, bd_crd
    Produces
    bd_pcz
  10. 10Compress DMD trajectory with PCA (PCZ format)
    Consumes
    pcz_zip_dmd_config, ca_pdb, dmd_crd
    Produces
    dmd_pcz
  11. 11Compress NMA trajectory with PCA (PCZ format)
    Consumes
    pcz_zip_nma_config, ca_pdb, nma_crd
    Produces
    nma_pcz
  12. 12Decompress BD PCZ trajectory back to CRD
    Consumes
    bd_pcz
    Produces
    bd_crd_uncompressed
  13. 13Decompress DMD PCZ trajectory back to CRD
    Consumes
    dmd_pcz
    Produces
    dmd_crd_uncompressed
  14. 14Decompress NMA PCZ trajectory back to CRD
    Consumes
    nma_pcz
    Produces
    nma_crd_uncompressed
  15. 15Compute RMSD for decompressed BD trajectory
    Consumes
    cpptraj_rms_bd_unc_config, ca_pdb, bd_crd_uncompressed
    Produces
    bd_uncompressed_rmsd, bd_xtc_uncompressed
  16. 16Compute RMSD for decompressed DMD trajectory
    Consumes
    cpptraj_rms_dmd_unc_config, ca_pdb, dmd_crd_uncompressed
    Produces
    dmd_uncompressed_rmsd, dmd_xtc_uncompressed
  17. 17Compute RMSD for decompressed NMA trajectory
    Consumes
    cpptraj_rms_nma_unc_config, ca_pdb, nma_crd_uncompressed
    Produces
    nma_uncompressed_rmsd, nma_xtc_uncompressed
  18. 18Extract PCA information from NMA PCZ file
    Consumes
    nma_pcz
    Produces
    pcz_report
  19. 19Extract eigenvectors from NMA PCZ file
    Consumes
    pcz_evecs_config, nma_pcz
    Produces
    pcz_evecs_report
  20. 20Animate NMA principal component eigenvector 1
    Consumes
    pcz_animate_config, nma_pcz
    Produces
    proj1_crd
  21. 21Convert PC1 animation trajectory to XTC format
    Consumes
    cpptraj_convert_proj1_config, ca_pdb, proj1_crd
    Produces
    proj1_xtc
  22. 22Compute B-factors from all NMA principal components
    Consumes
    pcz_bfactor_all_config, nma_pcz
    Produces
    bfactor_all_dat, bfactor_all_pdb
  23. 23Compute B-factors from NMA principal component 1
    Consumes
    pcz_bfactor_mode1_config, nma_pcz
    Produces
    bfactor_mode1_dat, bfactor_mode1_pdb
  24. 24Compute B-factors from NMA principal component 2
    Consumes
    pcz_bfactor_mode2_config, nma_pcz
    Produces
    bfactor_mode2_dat, bfactor_mode2_pdb
  25. 25Compute B-factors from NMA principal component 3
    Consumes
    pcz_bfactor_mode3_config, nma_pcz
    Produces
    bfactor_mode3_dat, bfactor_mode3_pdb
  26. 26Compute B-factors from NMA principal component 4
    Consumes
    pcz_bfactor_mode4_config, nma_pcz
    Produces
    bfactor_mode4_dat, bfactor_mode4_pdb
  27. 27Compute B-factors from NMA principal component 5
    Consumes
    pcz_bfactor_mode5_config, nma_pcz
    Produces
    bfactor_mode5_dat, bfactor_mode5_pdb
  28. 28Detect hinge regions in BD trajectory (B-factor slope method)
    Consumes
    pcz_hinges_bfactor_config, bd_pcz
    Produces
    hinges_bfactor_report
  29. 29Detect hinge regions in BD trajectory (dynamic domain method)
    Consumes
    pcz_hinges_dyndom_config, bd_pcz
    Produces
    hinges_dyndom_report
  30. 30Detect hinge regions in BD trajectory (force constant method)
    Consumes
    pcz_hinges_fcte_config, bd_pcz
    Produces
    hinges_fcte_report
  31. 31Compute apparent stiffness from NMA PCZ trajectory
    Consumes
    pcz_stiffness_config, nma_pcz
    Produces
    stiffness_report
  32. 32Compute collectivity index from NMA PCZ trajectory
    Consumes
    pcz_collectivity_config, nma_pcz
    Produces
    pcz_collectivity_report
  33. 33Compare PCZ similarity BD vs BD
    Consumes
    bd_pcz_1, bd_pcz_2
    Produces
    similarity_bd_bd
  34. 34Compare PCZ similarity BD vs DMD
    Consumes
    bd_pcz, dmd_pcz
    Produces
    similarity_bd_dmd
  35. 35Compare PCZ similarity BD vs NMA
    Consumes
    bd_pcz, nma_pcz
    Produces
    similarity_bd_nma
  36. 36Compare PCZ similarity BD vs MD (MoDEL)
    Consumes
    bd_pcz, md_pcz
    Produces
    similarity_bd_md
  37. 37Compare PCZ similarity DMD vs BD
    Consumes
    dmd_pcz, bd_pcz
    Produces
    similarity_dmd_bd
  38. 38Compare PCZ similarity DMD vs DMD
    Consumes
    dmd_pcz_1, dmd_pcz_2
    Produces
    similarity_dmd_dmd
  39. 39Compare PCZ similarity DMD vs NMA
    Consumes
    dmd_pcz, nma_pcz
    Produces
    similarity_dmd_nma
  40. 40Compare PCZ similarity DMD vs MD (MoDEL)
    Consumes
    dmd_pcz, md_pcz
    Produces
    similarity_dmd_md
  41. 41Compare PCZ similarity NMA vs BD
    Consumes
    nma_pcz, bd_pcz
    Produces
    similarity_nma_bd
  42. 42Compare PCZ similarity NMA vs DMD
    Consumes
    nma_pcz, dmd_pcz
    Produces
    similarity_nma_dmd
  43. 43Compare PCZ similarity NMA vs NMA
    Consumes
    nma_pcz_1, nma_pcz_2
    Produces
    similarity_nma_nma
  44. 44Compare PCZ similarity NMA vs MD (MoDEL)
    Consumes
    nma_pcz, md_pcz
    Produces
    similarity_nma_md
  45. 45Compare PCZ similarity MD (MoDEL) vs BD
    Consumes
    md_pcz, bd_pcz
    Produces
    similarity_md_bd
  46. 46Compare PCZ similarity MD (MoDEL) vs DMD
    Consumes
    md_pcz, dmd_pcz
    Produces
    similarity_md_dmd
  47. 47Compare PCZ similarity MD (MoDEL) vs NMA
    Consumes
    md_pcz, nma_pcz
    Produces
    similarity_md_nma
  48. 48Compare PCZ similarity MD (MoDEL) vs MD (MoDEL)
    Consumes
    md_pcz_1, md_pcz_2
    Produces
    similarity_md_md

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