CWL Macromolecular Coarse-Grained Flexibility tutorial
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Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

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SEEK ID: https://workflowhub.eu/workflows/552?version=1

DOI: 10.48546/workflowhub.workflow.552.1

Inputs

ID Name Description Type
step0_extract_atoms_input_structure_path Input file Input structure file path.
  • File
step0_extract_atoms_output_structure_path Output file Output structure file path.
  • string
step0_extract_atoms_config Config file Configuration file for biobb_structure_utils.extract_atoms tool.
  • string
step1_bd_run_output_crd_path Output file Output ensemble.
  • string
step1_bd_run_output_log_path Output file Output log file.
  • string
step1_bd_run_config Config file Configuration file for biobb_flexserv.bd_run tool.
  • string
step2_cpptraj_rms_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step2_cpptraj_rms_output_traj_path Output file Path to the output processed trajectory.
  • string
step2_cpptraj_rms_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step3_dmd_run_output_crd_path Output file Output ensemble.
  • string
step3_dmd_run_output_log_path Output file Output log file.
  • string
step4_cpptraj_rms_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step4_cpptraj_rms_output_traj_path Output file Path to the output processed trajectory.
  • string
step4_cpptraj_rms_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step5_nma_run_output_crd_path Output file Output ensemble.
  • string
step5_nma_run_output_log_path Output file Output log file.
  • string
step5_nma_run_config Config file Configuration file for biobb_flexserv.nma_run tool.
  • string
step6_cpptraj_rms_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step6_cpptraj_rms_output_traj_path Output file Path to the output processed trajectory.
  • string
step6_cpptraj_rms_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step7_pcz_zip_output_pcz_path Output file Output compressed trajectory.
  • string
step7_pcz_zip_config Config file Configuration file for biobb_flexserv.pcz_zip tool.
  • string
step8_pcz_zip_output_pcz_path Output file Output compressed trajectory.
  • string
step8_pcz_zip_config Config file Configuration file for biobb_flexserv.pcz_zip tool.
  • string
step9_pcz_zip_output_pcz_path Output file Output compressed trajectory.
  • string
step9_pcz_zip_config Config file Configuration file for biobb_flexserv.pcz_zip tool.
  • string
step10_pcz_unzip_output_crd_path Output file Output uncompressed trajectory.
  • string
step11_pcz_unzip_output_crd_path Output file Output uncompressed trajectory.
  • string
step12_pcz_unzip_output_crd_path Output file Output uncompressed trajectory.
  • string
step13_cpptraj_rms_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step13_cpptraj_rms_output_traj_path Output file Path to the output processed trajectory.
  • string
step13_cpptraj_rms_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step14_cpptraj_rms_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step14_cpptraj_rms_output_traj_path Output file Path to the output processed trajectory.
  • string
step14_cpptraj_rms_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step15_cpptraj_rms_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step15_cpptraj_rms_output_traj_path Output file Path to the output processed trajectory.
  • string
step15_cpptraj_rms_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step16_pcz_info_output_json_path Output file Output json file with PCA info such as number of components, variance and dimensionality.
  • string
step17_pcz_evecs_output_json_path Output file Output json file with PCA Eigen Vectors.
  • string
step17_pcz_evecs_config Config file Configuration file for biobb_flexserv.pcz_evecs tool.
  • string
step18_pcz_animate_output_crd_path Output file Output PCA animated trajectory file.
  • string
step18_pcz_animate_config Config file Configuration file for biobb_flexserv.pcz_animate tool.
  • string
step19_cpptraj_convert_output_cpptraj_path Output file Path to the output processed trajectory.
  • string
step19_cpptraj_convert_config Config file Configuration file for biobb_analysis.cpptraj_convert tool.
  • string
step20_pcz_bfactor_output_dat_path Output file Output Bfactor x residue x PCA mode file.
  • string
step20_pcz_bfactor_output_pdb_path Output file Output PDB with Bfactor x residue x PCA mode file.
  • string
step20_pcz_bfactor_config Config file Configuration file for biobb_flexserv.pcz_bfactor tool.
  • string
step21_pcz_hinges_output_json_path Output file Output hinge regions x PCA mode file.
  • string
step21_pcz_hinges_config Config file Configuration file for biobb_flexserv.pcz_hinges tool.
  • string
step22_pcz_hinges_output_json_path Output file Output hinge regions x PCA mode file.
  • string
step22_pcz_hinges_config Config file Configuration file for biobb_flexserv.pcz_hinges tool.
  • string
step23_pcz_hinges_output_json_path Output file Output hinge regions x PCA mode file.
  • string
step23_pcz_hinges_config Config file Configuration file for biobb_flexserv.pcz_hinges tool.
  • string
step24_pcz_stiffness_output_json_path Output file Output json file with PCA Stiffness.
  • string
step24_pcz_stiffness_config Config file Configuration file for biobb_flexserv.pcz_stiffness tool.
  • string
step25_pcz_collectivity_output_json_path Output file Output json file with PCA Collectivity indexes per mode.
  • string
step25_pcz_collectivity_config Config file Configuration file for biobb_flexserv.pcz_collectivity tool.
  • string
step26_pcz_similarity_input_pcz_path2 Input file Input compressed trajectory file 2.
  • File
step26_pcz_similarity_output_json_path Output file Output json file with PCA Similarity results.
  • string
step27_pcz_similarity_input_pcz_path2 Input file Input compressed trajectory file 2.
  • File
step27_pcz_similarity_output_json_path Output file Output json file with PCA Similarity results.
  • string
step28_pcz_similarity_input_pcz_path2 Input file Input compressed trajectory file 2.
  • File
step28_pcz_similarity_output_json_path Output file Output json file with PCA Similarity results.
  • string

Steps

ID Name Description
step0_extract_atoms extract_atoms Class to extract atoms from a 3D structure.
step1_bd_run bd_run Run Brownian Dynamics from FlexServ
step2_cpptraj_rms cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step3_dmd_run dmd_run Run Discrete Molecular Dynamics from FlexServ
step4_cpptraj_rms cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step5_nma_run nma_run Run Normal Mode Analysis from FlexServ
step6_cpptraj_rms cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step7_pcz_zip pcz_zip Compress MD simulation trajectories with PCA suite
step8_pcz_zip pcz_zip Compress MD simulation trajectories with PCA suite
step9_pcz_zip pcz_zip Compress MD simulation trajectories with PCA suite
step10_pcz_unzip pcz_unzip Uncompress MD simulation trajectories with PCA suite
step11_pcz_unzip pcz_unzip Uncompress MD simulation trajectories with PCA suite
step12_pcz_unzip pcz_unzip Uncompress MD simulation trajectories with PCA suite
step13_cpptraj_rms cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step14_cpptraj_rms cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step15_cpptraj_rms cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step16_pcz_info pcz_info Extract PCA info (variance, Dimensionality) from a compressed PCZ file
step17_pcz_evecs pcz_evecs Extract PCA Eigen Vectors from a compressed PCZ file
step18_pcz_animate pcz_animate Extract PCA animations from a compressed PCZ file
step19_cpptraj_convert cpptraj_convert Wrapper of the Ambertools Cpptraj module for converting between cpptraj compatible trajectory file formats and/or extracting a selection of atoms or frames.
step20_pcz_bfactor pcz_bfactor Extract residue bfactors x PCA mode from a compressed PCZ file
step21_pcz_hinges pcz_hinges Compute possible hinge regions (residues around which large protein movements are organized) of a molecule from a compressed PCZ file
step22_pcz_hinges pcz_hinges Compute possible hinge regions (residues around which large protein movements are organized) of a molecule from a compressed PCZ file
step23_pcz_hinges pcz_hinges Compute possible hinge regions (residues around which large protein movements are organized) of a molecule from a compressed PCZ file
step24_pcz_stiffness pcz_stiffness Extract PCA stiffness from a compressed PCZ file
step25_pcz_collectivity pcz_collectivity Extract PCA collectivity (numerical measure of how many atoms are affected by a given mode) from a compressed PCZ file
step26_pcz_similarity pcz_similarity Compute PCA similarity between two given compressed PCZ files
step27_pcz_similarity pcz_similarity Compute PCA similarity between two given compressed PCZ files
step28_pcz_similarity pcz_similarity Compute PCA similarity between two given compressed PCZ files

Outputs

ID Name Description Type
step0_extract_atoms_out1 output_structure_path Output structure file path.
  • File
step1_bd_run_out1 output_crd_path Output ensemble.
  • File
step1_bd_run_out2 output_log_path Output log file.
  • File
step2_cpptraj_rms_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step2_cpptraj_rms_out2 output_traj_path Path to the output processed trajectory.
  • File
step3_dmd_run_out1 output_crd_path Output ensemble.
  • File
step3_dmd_run_out2 output_log_path Output log file.
  • File
step4_cpptraj_rms_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step4_cpptraj_rms_out2 output_traj_path Path to the output processed trajectory.
  • File
step5_nma_run_out1 output_crd_path Output ensemble.
  • File
step5_nma_run_out2 output_log_path Output log file.
  • File
step6_cpptraj_rms_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step6_cpptraj_rms_out2 output_traj_path Path to the output processed trajectory.
  • File
step7_pcz_zip_out1 output_pcz_path Output compressed trajectory.
  • File
step8_pcz_zip_out1 output_pcz_path Output compressed trajectory.
  • File
step9_pcz_zip_out1 output_pcz_path Output compressed trajectory.
  • File
step10_pcz_unzip_out1 output_crd_path Output uncompressed trajectory.
  • File
step11_pcz_unzip_out1 output_crd_path Output uncompressed trajectory.
  • File
step12_pcz_unzip_out1 output_crd_path Output uncompressed trajectory.
  • File
step13_cpptraj_rms_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step13_cpptraj_rms_out2 output_traj_path Path to the output processed trajectory.
  • File
step14_cpptraj_rms_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step14_cpptraj_rms_out2 output_traj_path Path to the output processed trajectory.
  • File
step15_cpptraj_rms_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step15_cpptraj_rms_out2 output_traj_path Path to the output processed trajectory.
  • File
step16_pcz_info_out1 output_json_path Output json file with PCA info such as number of components, variance and dimensionality.
  • File
step17_pcz_evecs_out1 output_json_path Output json file with PCA Eigen Vectors.
  • File
step18_pcz_animate_out1 output_crd_path Output PCA animated trajectory file.
  • File
step19_cpptraj_convert_out1 output_cpptraj_path Path to the output processed trajectory.
  • File
step20_pcz_bfactor_out1 output_dat_path Output Bfactor x residue x PCA mode file.
  • File
step20_pcz_bfactor_out2 output_pdb_path Output PDB with Bfactor x residue x PCA mode file.
  • File
step21_pcz_hinges_out1 output_json_path Output hinge regions x PCA mode file.
  • File
step22_pcz_hinges_out1 output_json_path Output hinge regions x PCA mode file.
  • File
step23_pcz_hinges_out1 output_json_path Output hinge regions x PCA mode file.
  • File
step24_pcz_stiffness_out1 output_json_path Output json file with PCA Stiffness.
  • File
step25_pcz_collectivity_out1 output_json_path Output json file with PCA Collectivity indexes per mode.
  • File
step26_pcz_similarity_out1 output_json_path Output json file with PCA Similarity results.
  • File
step27_pcz_similarity_out1 output_json_path Output json file with PCA Similarity results.
  • File
step28_pcz_similarity_out1 output_json_path Output json file with PCA Similarity results.
  • File

Version History

Version 1 (earliest) Created 2nd Aug 2023 at 11:50 by Genís Bayarri

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Citation
Hospital, A., & Bayarri, G. (2023). CWL Macromolecular Coarse-Grained Flexibility tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.552.1
License
Apache License 2.0
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Views: 2216   Downloads: 578

Created: 2nd Aug 2023 at 11:50

Last updated: 2nd Aug 2023 at 12:13

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