CWL Protein Conformational Transitions calculations tutorial Version 1
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Download RO-CrateProtein 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.
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. |
|
| step0_extract_chain_output_structure_path | Output file | Output structure file path. |
|
| step0_extract_chain_config | Config file | Configuration file for biobb_structure_utils.extract_chain tool. |
|
| step1_extract_chain_input_structure_path | Input file | Input structure file path. |
|
| step1_extract_chain_output_structure_path | Output file | Output structure file path. |
|
| step1_extract_chain_config | Config file | Configuration file for biobb_structure_utils.extract_chain tool. |
|
| step2_remove_molecules_output_molecules_path | Output file | Output molcules file path. |
|
| 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. |
|
| 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. |
|
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. |
|
| step1_extract_chain_out1 | output_structure_path | Output structure file path. |
|
| step2_remove_molecules_out1 | output_molecules_path | Output molcules file path. |
|
| 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. |
|
Version History
Version 1 (earliest) Created 2nd Aug 2023 at 10:54 by Genís Bayarri
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Views: 2781 Downloads: 813
Created: 2nd Aug 2023 at 10:54
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https://orcid.org/0000-0003-0513-0288
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
