Workflow Type: Galaxy
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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.
Steps
ID | Name | Description |
---|---|---|
0 | Fetch origin | biobb_io_pdb_ext |
1 | Fetch target | biobb_io_pdb_ext |
2 | ExtractChain origin | biobb_structure_utils_extract_chain_ext |
3 | ExtractChain target | biobb_structure_utils_extract_chain_ext |
4 | RemoveMolecules origin | biobb_structure_utils_remove_molecules_ext |
5 | GodmdPrep | biobb_godmd_godmd_prep_ext |
6 | GodmdRun | biobb_godmd_godmd_run_ext |
7 | CpptrajConvert | biobb_analysis_cpptraj_convert_ext |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
mygodmd_prep.aln | #main/mygodmd_prep.aln | n/a |
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origin-target.godmd.dcd | #main/origin-target.godmd.dcd | n/a |
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origin-target.godmd.ene.out | #main/origin-target.godmd.ene.out | n/a |
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origin-target.godmd.log | #main/origin-target.godmd.log | n/a |
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origin-target.godmd.mdcrd | #main/origin-target.godmd.mdcrd | n/a |
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origin-target.godmd.pdb | #main/origin-target.godmd.pdb | n/a |
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origin.chains.nolig.pdb | #main/origin.chains.nolig.pdb | n/a |
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origin.chains.pdb | #main/origin.chains.pdb | n/a |
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origin.pdb | #main/origin.pdb | n/a |
|
target.chains.pdb | #main/target.chains.pdb | n/a |
|
target.pdb | #main/target.pdb | n/a |
|
Version History
Version 1 (earliest) Created 11th Aug 2023 at 09:36 by Genís Bayarri
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Citation
Hospital, A., & Bayarri, G. (2023). Galaxy Protein Conformational Transitions calculations tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.558.1
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Views: 3117 Downloads: 311 Runs: 0
Created: 11th Aug 2023 at 09:36
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