Protein-ligand docking (fpocket)
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).

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SEEK ID: https://workflowhub.eu/workflows/257?version=1

DOI: 10.48546/workflowhub.workflow.257.1

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

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.

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