Workflow Type: Galaxy
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Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, 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 structure | biobb_io_pdb_ext |
1 | ExtractAtoms | biobb_structure_utils_extract_atoms_ext |
2 | NmaRun | biobb_flexserv_nma_run_ext |
3 | DmdRun | biobb_flexserv_dmd_run_ext |
4 | BdRun | biobb_flexserv_bd_run_ext |
5 | CpptrajRms NMA | biobb_analysis_cpptraj_rms_ext |
6 | PczZip NMA | biobb_flexserv_pcz_zip_ext |
7 | CpptrajRms DMD | biobb_analysis_cpptraj_rms_ext |
8 | PczZip DMD | biobb_flexserv_pcz_zip_ext |
9 | CpptrajRms BD | biobb_analysis_cpptraj_rms_ext |
10 | PczZip BD | biobb_flexserv_pcz_zip_ext |
11 | PczUnzip NMA | biobb_flexserv_pcz_unzip_ext |
12 | PczBfactor NMA | biobb_flexserv_pcz_bfactor_ext |
13 | PczAnimate NMA | biobb_flexserv_pcz_animate_ext |
14 | PczInfo NMA | biobb_flexserv_pcz_info_ext |
15 | PczEvecs NMA | biobb_flexserv_pcz_evecs_ext |
16 | PczStiffness NMA | biobb_flexserv_pcz_stiffness_ext |
17 | PczCollectivity NMA | biobb_flexserv_pcz_collectivity_ext |
18 | PczUnzip DMD | biobb_flexserv_pcz_unzip_ext |
19 | PczUnzip BD | biobb_flexserv_pcz_unzip_ext |
20 | PczHinges DynDon | biobb_flexserv_pcz_hinges_ext |
21 | PczHinges Bfactor | biobb_flexserv_pcz_hinges_ext |
22 | PczHinges FCTE | biobb_flexserv_pcz_hinges_ext |
23 | CpptrajRms NMA 2 | biobb_analysis_cpptraj_rms_ext |
24 | CpptrajConvert NMA | biobb_analysis_cpptraj_convert_ext |
25 | CpptrajRms DMD 2 | biobb_analysis_cpptraj_rms_ext |
26 | CpptrajRms BD 2 | biobb_analysis_cpptraj_rms_ext |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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_anonymous_output_10 | #main/_anonymous_output_10 | n/a |
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_anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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_anonymous_output_12 | #main/_anonymous_output_12 | n/a |
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_anonymous_output_13 | #main/_anonymous_output_13 | n/a |
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_anonymous_output_14 | #main/_anonymous_output_14 | n/a |
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_anonymous_output_15 | #main/_anonymous_output_15 | n/a |
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_anonymous_output_16 | #main/_anonymous_output_16 | n/a |
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_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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_anonymous_output_7 | #main/_anonymous_output_7 | n/a |
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_anonymous_output_8 | #main/_anonymous_output_8 | n/a |
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_anonymous_output_9 | #main/_anonymous_output_9 | n/a |
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bd_ensemble.log | #main/bd_ensemble.log | n/a |
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bd_ensemble.mdcrd | #main/bd_ensemble.mdcrd | n/a |
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bd_ensemble.pcz | #main/bd_ensemble.pcz | n/a |
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bd_ensemble_rmsd.dat | #main/bd_ensemble_rmsd.dat | n/a |
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bd_ensemble_rmsd.dcd | #main/bd_ensemble_rmsd.dcd | n/a |
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bd_ensemble_uncompressed.crd | #main/bd_ensemble_uncompressed.crd | n/a |
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bfactor_all.dat | #main/bfactor_all.dat | n/a |
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bfactor_all.pdb | #main/bfactor_all.pdb | n/a |
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dmd_ensemble.log | #main/dmd_ensemble.log | n/a |
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dmd_ensemble.mdcrd | #main/dmd_ensemble.mdcrd | n/a |
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hinges_bfactor_report.json | #main/hinges_bfactor_report.json | n/a |
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mypdb.pdb | #main/mypdb.pdb | n/a |
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nma_ensemble.log | #main/nma_ensemble.log | n/a |
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nma_ensemble.mdcrd | #main/nma_ensemble.mdcrd | n/a |
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pcz_collectivity.json | #main/pcz_collectivity.json | n/a |
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pcz_evecs.json | #main/pcz_evecs.json | n/a |
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pcz_proj1.crd | #main/pcz_proj1.crd | n/a |
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pcz_proj1.dcd | #main/pcz_proj1.dcd | n/a |
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pcz_report.json | #main/pcz_report.json | n/a |
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pcz_stiffness.json | #main/pcz_stiffness.json | n/a |
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structure_ca.pdb | #main/structure_ca.pdb | n/a |
|
Version History
Version 1 (earliest) Created 11th Aug 2023 at 09:32 by Genís Bayarri
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Citation
Hospital, A., & Bayarri, G. (2023). Galaxy Macromolecular Coarse-Grained Flexibility tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.557.1
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Created: 11th Aug 2023 at 09:32
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