Galaxy Protein Conformational Transitions calculations tutorial
Version 1

Workflow Type: Galaxy
Stable

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.

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

Views: 1884   Downloads: 161

Created: 11th Aug 2023 at 09:36

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