Protein-ligand docking
Version 1

Workflow Type: Common Workflow Language
Stable

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

Inputs

ID Name Description Type
step1_fpocket_select_config n/a n/a
  • string
step1_fpocket_select_input_pockets_zip n/a n/a
  • File
step1_fpocket_select_output_pocket_pdb n/a n/a
  • string
step1_fpocket_select_output_pocket_pqr n/a n/a
  • string
step2_box_config n/a n/a
  • string
step2_box_output_pdb_path n/a n/a
  • string
step3_babel_convert_prep_lig_config n/a n/a
  • string
step3_babel_convert_prep_lig_input_path n/a n/a
  • File
step3_babel_convert_prep_lig_output_path n/a n/a
  • string
step4_str_check_add_hydrogens_config n/a n/a
  • string
step4_str_check_add_hydrogens_input_structure_path n/a n/a
  • File
step4_str_check_add_hydrogens_output_structure_path n/a n/a
  • string
step5_autodock_vina_run_output_pdbqt_path n/a n/a
  • string
step5_autodock_vina_run_output_log_path n/a n/a
  • string
step6_babel_convert_pose_pdb_config n/a n/a
  • string
step6_babel_convert_pose_pdb_output_path n/a n/a
  • string

Steps

ID Name Description
step1_fpocket_select FPocketSelect Selects a single pocket in the outputs of the fpocket building block..
step2_box Box This class sets the center and the size of a rectangular parallelepiped box around a set of residues or a pocket.
step3_babel_convert_prep_lig BabelConvert Small molecule format conversion.
step4_str_check_add_hydrogens StrCheckAddHydrogens This class is a wrapper of the Structure Checking tool to add hydrogens to a 3D structure.
step5_autodock_vina_run AutoDockVinaRun Wrapper of the AutoDock Vina software.
step6_babel_convert_pose_pdb BabelConvert Small molecule format conversion.

Outputs

ID Name Description Type
step1_fpocket_select_out1 output_pocket_pdb Path to the PDB file with the cavity found by fpocket
  • File
step1_fpocket_select_out2 output_pocket_pqr Path to the PQR file with the pocket found by fpocket
  • File
step2_box_out1 output_pdb_path PDB including the annotation of the box center and size as REMARKs
  • File
step3_babel_convert_prep_lig_out1 output_path Path to the output file
  • File
step4_str_check_add_hydrogens_out1 output_structure_path Output structure file path
  • File
step5_autodock_vina_run_out1 output_pdbqt_path Path to the output PDBQT file
  • File
step5_autodock_vina_run_out2 output_log_path Path to the log file
  • File
step6_babel_convert_pose_pdb_out1 output_path Path to the output file
  • File
Total size: 5.39 KB
help Creators and Submitter
Citation
Bayarri, G., & Hospital, A. (2022). Protein-ligand docking. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.259.1
Activity

Views: 79   Downloads: 0

Created: 10th Jan 2022 at 11:55

Last used: 26th Jan 2022 at 16:02

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Version History

Version 1 (earliest) Created 10th Jan 2022 at 11:55 by Genís Bayarri

Added/updated 1 files


Open master 51d0f41

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