Galaxy 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.

SEEK ID: https://workflowhub.eu/workflows/558?version=1

DOI: 10.48546/workflowhub.workflow.558.1

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	File
mygodmd_prep.aln	#main/mygodmd_prep.aln	n/a	File
origin-target.godmd.dcd	#main/origin-target.godmd.dcd	n/a	File
origin-target.godmd.ene.out	#main/origin-target.godmd.ene.out	n/a	File
origin-target.godmd.log	#main/origin-target.godmd.log	n/a	File
origin-target.godmd.mdcrd	#main/origin-target.godmd.mdcrd	n/a	File
origin-target.godmd.pdb	#main/origin-target.godmd.pdb	n/a	File
origin.chains.nolig.pdb	#main/origin.chains.nolig.pdb	n/a	File
origin.chains.pdb	#main/origin.chains.pdb	n/a	File
origin.pdb	#main/origin.pdb	n/a	File
target.chains.pdb	#main/target.chains.pdb	n/a	File
target.pdb	#main/target.pdb	n/a	File

Version History

Version 1 (earliest) Created 11th Aug 2023 at 09:36 by Genís Bayarri

Initial commit

Frozen Version-1 ec99201

Creators and Submitter

Creators

Submitter

Genís Bayarri

Discussion Channels

BioExcel Workflows

Galaxy

Documentation

Citation

Hospital, A., & Bayarri, G. (2023). Galaxy Protein Conformational Transitions calculations tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.558.1

License

Apache License 2.0 (Apache-2.0)

Activity

Views: 6917 Downloads: 976 Runs: 1

Created: 11th Aug 2023 at 09:36

Galaxy Protein Conformational Transitions calculations tutorial Version 1