Galaxy Molecular Structure Checking
Version 1

Workflow Type: Galaxy
Stable

Molecular Structure Checking using BioExcel Building Blocks (biobb)


This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

Structure checking is a key step before setting up a protein system for simulations. A number of common issues found in structures at Protein Data Bank may compromise the success of the simulation, or may suggest that longer equilibration procedures are necessary.

The workflow shows how to:

  • Run basic manipulations on structures (selection of models, chains, alternative locations
  • Detect and fix amide assignments and wrong chiralities
  • Detect and fix protein backbone issues (missing fragments, and atoms, capping)
  • Detect and fix missing side-chain atoms
  • Add hydrogen atoms according to several criteria
  • Detect and classify atomic clashes
  • Detect possible disulfide bonds (SS)

An implementation of this workflow in a web-based Graphical User Interface (GUI) can be found in the https://mmb.irbbarcelona.org/biobb-wfs/ server (see https://mmb.irbbarcelona.org/biobb-wfs/help/create/structure#check).


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 Pdb biobb_io_pdb_ext
1 CanonicalFasta biobb_io_canonical_fasta_ext
2 StructureCheck biobb_structure_utils_structure_check_ext
3 ExtractModel biobb_structure_utils_extract_model_ext
4 ExtractChain biobb_structure_utils_extract_chain_ext
5 FixAltlocs biobb_model_fix_altlocs_ext
6 FixSsbonds biobb_model_fix_ssbonds_ext
7 RemoveMolecules biobb_structure_utils_remove_molecules_ext
8 RemoveMolecules biobb_structure_utils_remove_molecules_ext
9 ReduceRemoveHydrogens biobb_chemistry_reduce_remove_hydrogens_ext
10 RemovePdbWater biobb_structure_utils_remove_pdb_water_ext
11 FixAmides biobb_model_fix_amides_ext
12 FixChirality biobb_model_fix_chirality_ext
13 FixSideChain biobb_model_fix_side_chain_ext
14 FixBackbone biobb_model_fix_backbone_ext
15 LeapGenTop biobb_amber_leap_gen_top_ext
16 SanderMdrun biobb_amber_sander_mdrun_ext
17 AmberToPdb biobb_amber_amber_to_pdb_ext
18 StructureCheck biobb_structure_utils_structure_check_ext

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
myamber_to_pdb.pdb #main/myamber_to_pdb.pdb n/a
  • File
mycanonical_fasta.fasta #main/mycanonical_fasta.fasta n/a
  • File
myextract_chain.pdb #main/myextract_chain.pdb n/a
  • File
myextract_model.pdb #main/myextract_model.pdb n/a
  • File
myfix_altlocs.pdb #main/myfix_altlocs.pdb n/a
  • File
myfix_amides.pdb #main/myfix_amides.pdb n/a
  • File
myfix_backbone.pdb #main/myfix_backbone.pdb n/a
  • File
myfix_chirality.pdb #main/myfix_chirality.pdb n/a
  • File
myfix_side_chain.pdb #main/myfix_side_chain.pdb n/a
  • File
myfix_ssbonds.pdb #main/myfix_ssbonds.pdb n/a
  • File
myleap_gen_top.crd #main/myleap_gen_top.crd n/a
  • File
myleap_gen_top.pdb #main/myleap_gen_top.pdb n/a
  • File
myleap_gen_top.top #main/myleap_gen_top.top n/a
  • File
mypdb.pdb #main/mypdb.pdb n/a
  • File
myreduce_remove_hydrogens.pdb #main/myreduce_remove_hydrogens.pdb n/a
  • File
myremove_molecules.pdb #main/myremove_molecules.pdb n/a
  • File
myremove_pdb_water.pdb #main/myremove_pdb_water.pdb n/a
  • File
mysander_mdrun.cpout #main/mysander_mdrun.cpout n/a
  • File
mysander_mdrun.cprst #main/mysander_mdrun.cprst n/a
  • File
mysander_mdrun.crd #main/mysander_mdrun.crd n/a
  • File
mysander_mdrun.log #main/mysander_mdrun.log n/a
  • File
mysander_mdrun.mdinfo #main/mysander_mdrun.mdinfo n/a
  • File
mysander_mdrun.rst #main/mysander_mdrun.rst n/a
  • File
mystructure_check.json #main/mystructure_check.json n/a
  • File

Version History

Version 1 (earliest) Created 5th Mar 2024 at 08:58 by Genís Bayarri

Initial commit


Frozen Version-1 afa1108
help Creators and Submitter
Citation
Hospital, A., & Bayarri, G. (2024). Galaxy Molecular Structure Checking. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.778.1
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Created: 5th Mar 2024 at 08:57

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