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.

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SEEK ID: https://workflowhub.eu/workflows/549?version=1

DOI: 10.48546/workflowhub.workflow.549.1

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
License
Apache Software License 2.0
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Views: 748

Created: 2nd Aug 2023 at 10:54

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