CWL Protein Conformational Transitions calculations tutorial
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Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, 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.

Click and drag the diagram to pan, double click or use the controls to zoom.

Inputs

ID Name Description Type
step0_extract_chain_input_structure_path Input file Input structure file path.
  • File
step0_extract_chain_output_structure_path Output file Output structure file path.
  • string
step0_extract_chain_config Config file Configuration file for biobb_structure_utils.extract_chain tool.
  • string
step1_extract_chain_input_structure_path Input file Input structure file path.
  • File
step1_extract_chain_output_structure_path Output file Output structure file path.
  • string
step1_extract_chain_config Config file Configuration file for biobb_structure_utils.extract_chain tool.
  • string
step2_remove_molecules_output_molecules_path Output file Output molcules file path.
  • string
step2_remove_molecules_config Config file Configuration file for biobb_structure_utils.remove_molecules tool.
  • string
step4_godmd_prep_output_aln_orig_path Output file Output GOdMD alignment file corresponding to the origin structure of the conformational transition.
  • string
step4_godmd_prep_output_aln_target_path Output file Output GOdMD alignment file corresponding to the target structure of the conformational transition.
  • string
step4_godmd_prep_config Config file Configuration file for biobb_godmd.godmd_prep tool.
  • string
step5_godmd_run_output_log_path Output file Output log file.
  • string
step5_godmd_run_output_ene_path Output file Output energy file.
  • string
step5_godmd_run_output_trj_path Output file Output trajectory file.
  • string
step5_godmd_run_output_pdb_path Output file Output structure file.
  • string
step5_godmd_run_config Config file Configuration file for biobb_godmd.godmd_run tool.
  • string
step6_cpptraj_convert_output_cpptraj_path Output file Path to the output processed trajectory.
  • string
step6_cpptraj_convert_config Config file Configuration file for biobb_analysis.cpptraj_convert tool.
  • string

Steps

ID Name Description
step0_extract_chain extract_chain This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure.
step1_extract_chain extract_chain This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure.
step2_remove_molecules remove_molecules Class to remove molecules from a 3D structure using Biopython.
step4_godmd_prep godmd_prep Helper BioBB to prepare inputs for the GOdMD tool (protein conformational transitions).
step5_godmd_run godmd_run Wrapper of the GOdMD tool to compute protein conformational transitions.
step6_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.

Outputs

ID Name Description Type
step0_extract_chain_out1 output_structure_path Output structure file path.
  • File
step1_extract_chain_out1 output_structure_path Output structure file path.
  • File
step2_remove_molecules_out1 output_molecules_path Output molcules file path.
  • File
step4_godmd_prep_out1 output_aln_orig_path Output GOdMD alignment file corresponding to the origin structure of the conformational transition.
  • File
step4_godmd_prep_out2 output_aln_target_path Output GOdMD alignment file corresponding to the target structure of the conformational transition.
  • File
step5_godmd_run_out1 output_log_path Output log file.
  • File
step5_godmd_run_out2 output_ene_path Output energy file.
  • File
step5_godmd_run_out3 output_trj_path Output trajectory file.
  • File
step5_godmd_run_out4 output_pdb_path Output structure file.
  • File
step6_cpptraj_convert_out1 output_cpptraj_path Path to the output processed trajectory.
  • File

Version History

Version 1 (earliest) Created 2nd Aug 2023 at 10:54 by Genís Bayarri

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Frozen Version-1 36c8c93
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Citation
Hospital, A., & Bayarri, G. (2023). CWL Protein Conformational Transitions calculations tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.549.1
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Created: 2nd Aug 2023 at 10:54

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