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).
- (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.
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
ID | Name | Description | Type |
---|---|---|---|
step0_structure_check_init_input_structure_path | Input file | Input structure file path. |
|
step0_structure_check_init_output_summary_path | Output file | Output summary checking results. |
|
step1_extract_model_input_structure_path | Input file | Input structure file path. |
|
step1_extract_model_output_structure_path | Output file | Output structure file path. |
|
step1_extract_model_config | Config file | Configuration file for biobb_structure_utils.extract_model tool. |
|
step2_extract_chain_output_structure_path | Output file | Output structure file path. |
|
step2_extract_chain_config | Config file | Configuration file for biobb_structure_utils.extract_chain tool. |
|
step3_fix_altlocs_output_pdb_path | Output file | Output PDB file path. |
|
step3_fix_altlocs_config | Config file | Configuration file for biobb_model.fix_altlocs tool. |
|
step4_fix_ssbonds_output_pdb_path | Output file | Output PDB file path. |
|
step5_remove_molecules_ions_output_molecules_path | Output file | Output molcules file path. |
|
step5_remove_molecules_ions_config | Config file | Configuration file for biobb_structure_utils.remove_molecules tool. |
|
step6_remove_molecules_ligands_output_molecules_path | Output file | Output molcules file path. |
|
step6_remove_molecules_ligands_config | Config file | Configuration file for biobb_structure_utils.remove_molecules tool. |
|
step7_reduce_remove_hydrogens_output_path | Output file | Path to the output file. |
|
step8_remove_pdb_water_output_pdb_path | Output file | Output PDB file path. |
|
step9_fix_amides_output_pdb_path | Output file | Output PDB file path. |
|
step10_fix_chirality_output_pdb_path | Output file | Output PDB file path. |
|
step11_fix_side_chain_output_pdb_path | Output file | Output PDB file path. |
|
step12_fix_backbone_input_fasta_canonical_sequence_path | Input file | Input FASTA file path. |
|
step12_fix_backbone_output_pdb_path | Output file | Output PDB file path. |
|
step13_leap_gen_top_output_pdb_path | Output file | Output 3D structure PDB file matching the topology file. |
|
step13_leap_gen_top_output_top_path | Output file | Output topology file (AMBER ParmTop). |
|
step13_leap_gen_top_output_crd_path | Output file | Output coordinates file (AMBER crd). |
|
step13_leap_gen_top_config | Config file | Configuration file for biobb_amber.leap_gen_top tool. |
|
step14_sander_mdrun_output_traj_path | Output file | Output trajectory file. |
|
step14_sander_mdrun_output_rst_path | Output file | Output restart file. |
|
step14_sander_mdrun_output_log_path | Output file | Output log file. |
|
step14_sander_mdrun_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step15_amber_to_pdb_output_pdb_path | Output file | Structure PDB file. |
|
step16_fix_pdb_output_pdb_path | Output file | Output PDB file path. |
|
step17_structure_check_output_summary_path | Output file | Output summary checking results. |
|
Steps
ID | Name | Description |
---|---|---|
step0_structure_check_init | structure_check | This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file. |
step1_extract_model | extract_model | This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure. |
step2_extract_chain | extract_chain | This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure. |
step3_fix_altlocs | fix_altlocs | Fix alternate locations from residues. |
step4_fix_ssbonds | fix_ssbonds | Fix SS bonds from residues. |
step5_remove_molecules_ions | remove_molecules | Class to remove molecules from a 3D structure using Biopython. |
step6_remove_molecules_ligands | remove_molecules | Class to remove molecules from a 3D structure using Biopython. |
step7_reduce_remove_hydrogens | reduce_remove_hydrogens | Removes hydrogen atoms to small molecules. |
step8_remove_pdb_water | remove_pdb_water | This class is a wrapper of the Structure Checking tool to remove water molecules from PDB 3D structures. |
step9_fix_amides | fix_amides | Creates a new PDB file flipping the clashing amide groups. |
step10_fix_chirality | fix_chirality | Creates a new PDB file fixing stereochemical errors in residue side-chains changing It's chirality. |
step11_fix_side_chain | fix_side_chain | Reconstructs the missing side chains and heavy atoms of the given PDB file. |
step12_fix_backbone | fix_backbone | Reconstructs the missing backbone atoms of the given PDB file. |
step13_leap_gen_top | leap_gen_top | Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package |
step14_sander_mdrun | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step15_amber_to_pdb | amber_to_pdb | Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package |
step16_fix_pdb | fix_pdb | Renumerates residues in a PDB structure according to a reference sequence from UniProt |
step17_structure_check | structure_check | This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file. |
Outputs
ID | Name | Description | Type |
---|---|---|---|
step0_structure_check_init_out1 | output_summary_path | Output summary checking results. |
|
step1_extract_model_out1 | output_structure_path | Output structure file path. |
|
step2_extract_chain_out1 | output_structure_path | Output structure file path. |
|
step3_fix_altlocs_out1 | output_pdb_path | Output PDB file path. |
|
step4_fix_ssbonds_out1 | output_pdb_path | Output PDB file path. |
|
step5_remove_molecules_ions_out1 | output_molecules_path | Output molcules file path. |
|
step6_remove_molecules_ligands_out1 | output_molecules_path | Output molcules file path. |
|
step7_reduce_remove_hydrogens_out1 | output_path | Path to the output file. |
|
step8_remove_pdb_water_out1 | output_pdb_path | Output PDB file path. |
|
step9_fix_amides_out1 | output_pdb_path | Output PDB file path. |
|
step10_fix_chirality_out1 | output_pdb_path | Output PDB file path. |
|
step11_fix_side_chain_out1 | output_pdb_path | Output PDB file path. |
|
step12_fix_backbone_out1 | output_pdb_path | Output PDB file path. |
|
step13_leap_gen_top_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file. |
|
step13_leap_gen_top_out2 | output_top_path | Output topology file (AMBER ParmTop). |
|
step13_leap_gen_top_out3 | output_crd_path | Output coordinates file (AMBER crd). |
|
step14_sander_mdrun_out1 | output_traj_path | Output trajectory file. |
|
step14_sander_mdrun_out2 | output_rst_path | Output restart file. |
|
step14_sander_mdrun_out3 | output_log_path | Output log file. |
|
step15_amber_to_pdb_out1 | output_pdb_path | Structure PDB file. |
|
step16_fix_pdb_out1 | output_pdb_path | Output PDB file path. |
|
step17_structure_check_out1 | output_summary_path | Output summary checking results. |
|
Version History
Version 1 (earliest) Created 5th Mar 2024 at 08:41 by Genís Bayarri
Initial commit
Frozen
Version-1
24d3421
Creators
Submitter
Views: 927 Downloads: 546
Created: 5th Mar 2024 at 08:41
This item has not yet been tagged.
None