Protein-ligand docking (fpocket)

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protein-ligand-docking-fpocket
protein-ligand-docking-fpocket
protein-ligand-docking-fpocket
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This workflow performs the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).

Code Snippets

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baseCommand: autodock_vina_run

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_vs:4.0.0--pyhdfd78af_2

inputs:
  input_ligand_pdbqt_path:
    label: Path to the input PDBQT ligand
    doc: |-
      Path to the input PDBQT ligand
      Type: string
      File type: input
      Accepted formats: pdbqt
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_ligand_pdbqt_path

  input_receptor_pdbqt_path:
    label: Path to the input PDBQT receptor
    doc: |-
      Path to the input PDBQT receptor
      Type: string
      File type: input
      Accepted formats: pdbqt
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --input_receptor_pdbqt_path

  input_box_path:
    label: Path to the PDB containig the residues belonging to the binding site
    doc: |-
      Path to the PDB containig the residues belonging to the binding site
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 3
      prefix: --input_box_path

  output_pdbqt_path:
    label: Path to the output PDBQT file
    doc: |-
      Path to the output PDBQT file
      Type: string
      File type: output
      Accepted formats: pdbqt
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 4
      prefix: --output_pdbqt_path
    default: system.pdbqt

  output_log_path:
    label: Path to the log file
    doc: |-
      Path to the log file
      Type: string
      File type: output
      Accepted formats: log
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log
    type: string
    format:
    - edam:format_2330
    inputBinding:
      prefix: --output_log_path
    default: system.log

  config:
    label: Advanced configuration options for biobb_vs AutoDockVinaRun
    doc: |-
      Advanced configuration options for biobb_vs AutoDockVinaRun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_vs AutoDockVinaRun documentation: https://biobb-vs.readthedocs.io/en/latest/vina.html#module-vina.autodock_vina_run
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_vs AutoDock Vina From line 11 of biobb_adapters/autodock_vina_run.cwl 
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baseCommand: babel_convert

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_chemistry:4.0.0--pyhdfd78af_1

inputs:
  input_path:
    label: Path to the input file
    doc: |-
      Path to the input file
      Type: string
      File type: input
      Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/babel/babel.smi
    type: File
    format:
    - edam:format_1637
    - edam:format_1476
    - edam:format_1929
    - edam:format_1929
    - edam:format_2033
    - edam:format_3878
    - edam:format_2030
    - edam:format_1477
    - edam:format_3815
    - edam:format_1477
    - edam:format_3815
    - edam:format_3816
    - edam:format_1476
    - edam:format_1476
    - edam:format_3603
    - edam:format_3814
    - edam:format_1196
    - edam:format_1196
    - edam:format_2033
    - edam:format_2332
    - edam:format_3875
    inputBinding:
      position: 1
      prefix: --input_path

  output_path:
    label: Path to the output file
    doc: |-
      Path to the output file
      Type: string
      File type: output
      Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/babel/ref_babel.convert.mol2
    type: string
    format:
    - edam:format_1476
    - edam:format_1929
    - edam:format_1929
    - edam:format_2033
    - edam:format_3878
    - edam:format_1477
    - edam:format_3815
    - edam:format_1477
    - edam:format_3815
    - edam:format_3816
    - edam:format_1476
    - edam:format_1476
    - edam:format_3603
    - edam:format_3814
    - edam:format_1196
    - edam:format_1196
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --output_path
    default: system.ent

  config:
    label: Advanced configuration options for biobb_chemistry BabelConvert
    doc: |-
      Advanced configuration options for biobb_chemistry BabelConvert. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_chemistry BabelConvert documentation: https://biobb-chemistry.readthedocs.io/en/latest/babelm.html#module-babelm.babel_convert
    type: string?
    inputBinding:
      prefix: --config
CWL Open Babel From line 11 of biobb_adapters/babel_convert.cwl 
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baseCommand: box

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_vs:4.0.0--pyhdfd78af_2

inputs:
  input_pdb_path:
    label: PDB file containing a selection of residue numbers or PQR file containing
      the pocket
    doc: |-
      PDB file containing a selection of residue numbers or PQR file containing the pocket
      Type: string
      File type: input
      Accepted formats: pdb, pqr
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box.pqr
    type: File
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_pdb_path:
    label: PDB including the annotation of the box center and size as REMARKs
    doc: |-
      PDB including the annotation of the box center and size as REMARKs
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_vs Box
    doc: |-
      Advanced configuration options for biobb_vs Box. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_vs Box documentation: https://biobb-vs.readthedocs.io/en/latest/utils.html#module-utils.box
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_vs From line 12 of biobb_adapters/box.cwl 
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baseCommand: fpocket_select

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_vs:4.0.0--pyhdfd78af_2

inputs:
  input_pockets_zip:
    label: Path to the pockets found by fpocket
    doc: |-
      Path to the pockets found by fpocket
      Type: string
      File type: input
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_pockets.zip
    type: File
    format:
    - edam:format_3987
    inputBinding:
      position: 1
      prefix: --input_pockets_zip

  output_pocket_pdb:
    label: Path to the PDB file with the cavity found by fpocket
    doc: |-
      Path to the PDB file with the cavity found by fpocket
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pocket.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pocket_pdb
    default: system.pdb

  output_pocket_pqr:
    label: Path to the PQR file with the pocket found by fpocket
    doc: |-
      Path to the PQR file with the pocket found by fpocket
      Type: string
      File type: output
      Accepted formats: pqr
      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pocket.pqr
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 3
      prefix: --output_pocket_pqr
    default: system.pqr

  config:
    label: Advanced configuration options for biobb_vs FPocketSelect
    doc: |-
      Advanced configuration options for biobb_vs FPocketSelect. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_vs FPocketSelect documentation: https://biobb-vs.readthedocs.io/en/latest/fpocket.html#module-fpocket.fpocket_select
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_vs Fpocket From line 11 of biobb_adapters/fpocket_select.cwl 
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baseCommand: str_check_add_hydrogens

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_structure_utils:4.0.0--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Input structure file path
    doc: |-
      Input structure file path
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/str_no_H.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_structure_path

  output_structure_path:
    label: Output structure file path
    doc: |-
      Output structure file path
      Type: string
      File type: output
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_str_H.pdbqt
    type: string
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_structure_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_structure_utils StrCheckAddHydrogens
    doc: |-
      Advanced configuration options for biobb_structure_utils StrCheckAddHydrogens. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils StrCheckAddHydrogens documentation: https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#utils-str-check-add-hydrogens-module
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_structure_utils From line 12 of biobb_adapters/str_check_add_hydrogens.cwl
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://workflowhub.eu/workflows/257
Name: protein-ligand-docking-fpocket
Version: Version 1
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Copyright: Public Domain
License: Boost Software License 1.0
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