Workflow Type: Common Workflow Language
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Stable
This workflow performs the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).
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Inputs
ID | Name | Description | Type |
---|---|---|---|
step1_fpocket_select_config | n/a | n/a |
|
step1_fpocket_select_input_pockets_zip | n/a | n/a |
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step1_fpocket_select_output_pocket_pdb | n/a | n/a |
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step1_fpocket_select_output_pocket_pqr | n/a | n/a |
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step2_box_config | n/a | n/a |
|
step2_box_output_pdb_path | n/a | n/a |
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step3_babel_convert_prep_lig_config | n/a | n/a |
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step3_babel_convert_prep_lig_input_path | n/a | n/a |
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step3_babel_convert_prep_lig_output_path | n/a | n/a |
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step4_str_check_add_hydrogens_config | n/a | n/a |
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step4_str_check_add_hydrogens_input_structure_path | n/a | n/a |
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step4_str_check_add_hydrogens_output_structure_path | n/a | n/a |
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step5_autodock_vina_run_output_pdbqt_path | n/a | n/a |
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step5_autodock_vina_run_output_log_path | n/a | n/a |
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step6_babel_convert_pose_pdb_config | n/a | n/a |
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step6_babel_convert_pose_pdb_output_path | n/a | n/a |
|
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 |
|
step1_fpocket_select_out2 | output_pocket_pqr | Path to the PQR file with the pocket found by fpocket |
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step2_box_out1 | output_pdb_path | PDB including the annotation of the box center and size as REMARKs |
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step3_babel_convert_prep_lig_out1 | output_path | Path to the output file |
|
step4_str_check_add_hydrogens_out1 | output_structure_path | Output structure file path |
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step5_autodock_vina_run_out1 | output_pdbqt_path | Path to the output PDBQT file |
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step5_autodock_vina_run_out2 | output_log_path | Path to the log file |
|
step6_babel_convert_pose_pdb_out1 | output_path | Path to the output file |
|
Version History
Version 1 (earliest) Created 10th Jan 2022 at 11:48 by Genís Bayarri
Added/updated 1 files
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Citation
Bayarri, G., & Hospital, A. (2022). Protein-ligand docking (fpocket). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.257.1
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Views: 1392 Downloads: 176
Created: 10th Jan 2022 at 11:48
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