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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).
- (c) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Inputs
ID | Name | Description | Type |
---|---|---|---|
step0_extract_chain_input_structure_path | Input file | Input structure file path. |
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step0_extract_chain_output_structure_path | Output file | Output structure file path. |
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step0_extract_chain_config | Config file | Configuration file for biobb_structure_utils.extract_chain tool. |
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step1_extract_chain_input_structure_path | Input file | Input structure file path. |
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step1_extract_chain_output_structure_path | Output file | Output structure file path. |
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step1_extract_chain_config | Config file | Configuration file for biobb_structure_utils.extract_chain tool. |
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step2_remove_molecules_output_molecules_path | Output file | Output molcules file path. |
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step2_remove_molecules_config | Config file | Configuration file for biobb_structure_utils.remove_molecules tool. |
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step4_godmd_prep_output_aln_orig_path | Output file | Output GOdMD alignment file corresponding to the origin structure of the conformational transition. |
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step4_godmd_prep_output_aln_target_path | Output file | Output GOdMD alignment file corresponding to the target structure of the conformational transition. |
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step4_godmd_prep_config | Config file | Configuration file for biobb_godmd.godmd_prep tool. |
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step5_godmd_run_output_log_path | Output file | Output log file. |
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step5_godmd_run_output_ene_path | Output file | Output energy file. |
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step5_godmd_run_output_trj_path | Output file | Output trajectory file. |
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step5_godmd_run_output_pdb_path | Output file | Output structure file. |
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step5_godmd_run_config | Config file | Configuration file for biobb_godmd.godmd_run tool. |
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step6_cpptraj_convert_output_cpptraj_path | Output file | Path to the output processed trajectory. |
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step6_cpptraj_convert_config | Config file | Configuration file for biobb_analysis.cpptraj_convert tool. |
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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. |
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step1_extract_chain_out1 | output_structure_path | Output structure file path. |
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step2_remove_molecules_out1 | output_molecules_path | Output molcules file path. |
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step4_godmd_prep_out1 | output_aln_orig_path | Output GOdMD alignment file corresponding to the origin structure of the conformational transition. |
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step4_godmd_prep_out2 | output_aln_target_path | Output GOdMD alignment file corresponding to the target structure of the conformational transition. |
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step5_godmd_run_out1 | output_log_path | Output log file. |
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step5_godmd_run_out2 | output_ene_path | Output energy file. |
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step5_godmd_run_out3 | output_trj_path | Output trajectory file. |
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step5_godmd_run_out4 | output_pdb_path | Output structure file. |
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step6_cpptraj_convert_out1 | output_cpptraj_path | Path to the output processed trajectory. |
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Version History
Version 1 (earliest) Created 2nd Aug 2023 at 10:54 by Genís Bayarri
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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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