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BioExcel FlexDyn - Protein Flexibility and Dynamics Analysis

W-19 · Protein Conformational Ensembles

v143 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.

  1. 01Download 1AKE structure from PDB
    Consumes
    fetch_pdb_config, src_conda_env_yaml
    Produces
    downloaded_pdb
  2. 02Extract first model from PDB
    Consumes
    extract_model_config, downloaded_pdb, src_conda_env_yaml
    Produces
    pdb_model
  3. 03Extract chain A monomer
    Consumes
    extract_chain_config, pdb_model, src_conda_env_yaml
    Produces
    monomer
  4. 04Extract backbone atoms from monomer
    Consumes
    cpptraj_mask_backbone_config, monomer, src_conda_env_yaml
    Produces
    prot_backbone
  5. 05Extract Cα atoms from monomer
    Consumes
    cpptraj_mask_ca_config, monomer, src_conda_env_yaml
    Produces
    prot_ca
  6. 06CONCOORD distance restraints calculation
    Consumes
    concoord_dist_config, monomer
    Produces
    concoord_dist_pdb, concoord_dist_gro, concoord_dist_dat
  7. 07CONCOORD structure ensemble generation
    Consumes
    concoord_disco_config, concoord_dist_pdb, concoord_dist_dat
    Produces
    concoord_disco_pdb, concoord_disco_rmsd, concoord_disco_bfactor
  8. 08RMSD analysis of CONCOORD ensemble
    Consumes
    cpptraj_rms_concoord_config, concoord_dist_pdb, concoord_disco_pdb, monomer, src_conda_env_yaml
    Produces
    concoord_rmsd
  9. 09Convert CONCOORD trajectory to TRR
    Consumes
    cpptraj_convert_concoord_config, concoord_dist_pdb, concoord_disco_pdb, src_conda_env_yaml
    Produces
    concoord_trr
  10. 10ProDy Anisotropic Network Model ensemble
    Consumes
    prody_anm_config, monomer
    Produces
    prody_ensemble
  11. 11RMSD analysis of ProDy ANM ensemble
    Consumes
    cpptraj_rms_prody_config, prody_ensemble, monomer, src_conda_env_yaml
    Produces
    prody_rmsd
  12. 12Convert ProDy ANM trajectory to TRR
    Consumes
    cpptraj_convert_prody_config, prot_backbone, prody_ensemble, src_conda_env_yaml
    Produces
    prody_trr
  13. 13FlexServ Brownian Dynamics simulation
    Consumes
    bd_run_config, prot_ca
    Produces
    bd_crd, bd_log
  14. 14RMSD analysis and fitting of BD trajectory
    Consumes
    cpptraj_rms_bd_config, prot_ca, bd_crd, monomer, src_conda_env_yaml
    Produces
    flexserv_bd_rmsd, flexserv_bd_traj_fitted
  15. 15FlexServ Discrete Molecular Dynamics simulation
    Consumes
    dmd_run_config, prot_ca
    Produces
    dmd_crd, dmd_log
  16. 16RMSD analysis and fitting of DMD trajectory
    Consumes
    cpptraj_rms_dmd_config, prot_ca, dmd_crd, monomer, src_conda_env_yaml
    Produces
    flexserv_dmd_rmsd, flexserv_dmd_traj_fitted
  17. 17FlexServ Normal Mode Analysis simulation
    Consumes
    nma_run_config, prot_ca
    Produces
    nma_crd, nma_log
  18. 18RMSD analysis of FlexServ NMA trajectory
    Consumes
    cpptraj_rms_nma_config, prot_ca, nma_crd, monomer, src_conda_env_yaml
    Produces
    flexserv_nma_rmsd
  19. 19Convert FlexServ NMA trajectory to TRR
    Consumes
    cpptraj_convert_nma_config, prot_ca, nma_crd, src_conda_env_yaml
    Produces
    nma_trr
  20. 20NOLB Non-Linear Rigid Block NMA ensemble
    Consumes
    nolb_nma_config, prot_ca
    Produces
    nolb_pdb
  21. 21RMSD analysis of NOLB ensemble
    Consumes
    cpptraj_rms_nolb_config, prot_ca, nolb_pdb, monomer, src_conda_env_yaml
    Produces
    nolb_rmsd
  22. 22Convert NOLB ensemble to TRR
    Consumes
    cpptraj_convert_nolb_config, prot_ca, nolb_pdb, src_conda_env_yaml
    Produces
    nolb_trr
  23. 23iMODS internal coordinates normal mode analysis
    Consumes
    imod_imode_config, monomer
    Produces
    imode_evecs
  24. 24iMODS internal coordinates Monte Carlo sampling
    Consumes
    imod_imc_config, monomer, imode_evecs
    Produces
    imc_pdb
  25. 25RMSD analysis of iMODS ensemble
    Consumes
    cpptraj_rms_imods_config, imc_pdb, monomer, src_conda_env_yaml
    Produces
    imods_rmsd
  26. 26Convert iMODS trajectory to TRR
    Consumes
    cpptraj_convert_imods_config, imc_pdb, src_conda_env_yaml
    Produces
    imods_trr
  27. 27Zip ensemble trajectories for concatenation
    Consumes
    concoord_trr, prody_trr, imods_trr, flexserv_dmd_traj_fitted, nma_trr, src_conda_env_yaml
    Produces
    concat_traj_zip
  28. 28Concatenate all ensemble trajectories
    Consumes
    concat_traj_zip, src_conda_env_yaml
    Produces
    concat_trr
  29. 29Create GROMACS index file for Cα atoms
    Consumes
    make_ndx_config, prot_ca, src_conda_env_yaml
    Produces
    gmx_index_file
  30. 30Cluster analysis of concatenated trajectory
    Consumes
    gmx_cluster_config, prot_ca, concat_trr, gmx_index_file, src_conda_env_yaml
    Produces
    cluster_concat_pdb
  31. 31RMSD fitting of meta-trajectory cluster representatives
    Consumes
    cpptraj_rms_meta_config, prot_ca, cluster_concat_pdb, src_conda_env_yaml
    Produces
    meta_traj_rmsd, meta_traj_fitted
  32. 32PCA compression of meta-trajectory (classical RMSd fitting)
    Consumes
    pcz_zip_classic_config, prot_ca, meta_traj_fitted
    Produces
    concat_pcz
  33. 33PCA compression of meta-trajectory (Gaussian weighted RMSd fitting)
    Consumes
    pcz_zip_gaussian_config, prot_ca, meta_traj_fitted
    Produces
    concat_pcz_gaussian
  34. 34Extract PCA statistics and variance profile
    Consumes
    concat_pcz
    Produces
    pcz_report
  35. 35Extract PCA eigenvectors
    Consumes
    pcz_evecs_config, concat_pcz
    Produces
    pcz_evecs_report
  36. 36Generate animation along first principal component
    Consumes
    pcz_animate_config, concat_pcz
    Produces
    proj1_crd
  37. 37Convert PC1 projection trajectory to XTC
    Consumes
    cpptraj_convert_proj_config, prot_ca, proj1_crd, src_conda_env_yaml
    Produces
    proj1_xtc
  38. 38B-factor analysis from PCA modes
    Consumes
    pcz_bfactor_config, concat_pcz
    Produces
    bfactor_all_dat, bfactor_all_pdb
  39. 39Hinge detection using B-factor slope method
    Consumes
    pcz_hinges_bfactor_config, concat_pcz_gaussian
    Produces
    hinges_bfactor_report
  40. 40Hinge detection using Dynamic Domain decomposition method
    Consumes
    pcz_hinges_dyndom_config, concat_pcz_gaussian
    Produces
    hinges_dyndom_report
  41. 41Hinge detection using Force Constant method
    Consumes
    pcz_hinges_fcte_config, concat_pcz_gaussian
    Produces
    hinges_fcte_report
  42. 42Apparent stiffness analysis from PCA
    Consumes
    pcz_stiffness_config, concat_pcz
    Produces
    stiffness_report
  43. 43Collectivity index analysis from PCA
    Consumes
    pcz_collectivity_config, concat_pcz
    Produces
    pcz_collectivity_report

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