Galaxy | BIOBB | Published Workflow | Fpocket Protein-Ligand Docking

Fpocket Protein-Ligand Docking

Annotation:

Step	Annotation
Step 1: Pdb output PDB name mypdb.pdb Take tool settings: Manual Input Properties Input: pdb_code 3HEC filter [ATOM, HETATM] api_id pdbe - PDB in Europe REST API
Step 2: IdealSdf output SDF name myideal_sdf.sdf Take tool settings: Manual Input Properties Input: ligand_code STI api_id pdb - RCSB PDB REST API
Step 3: ExtractMolecule input PDB,PDBQT file Output dataset 'output_pdb_path' from step 1 output PDB,PDBQT name myextract_molecule.pdb Take tool settings: Manual Input Properties Input: molecule_type protein chains [] binary_path check_structure output_format pdb
Step 4: BabelConvert input DAT,ENT,FA,FASTA,GRO,INP,LOG,MCIF,MDL,MMCIF,MOL,MOL2,PDB,PDBQT,PNG,SDF,SMI,SMILES,TXT,XML,XTC file Output dataset 'output_sdf_path' from step 2 output ENT,FA,FASTA,GRO,INP,MCIF,MDL,MMCIF,MOL,MOL2,PDB,PDBQT,PNG,SDF,SMI,SMILES,TXT name mybabel_convert.pdb Take tool settings: Manual Input Properties Input: input_format sdf - One of a family of chemical-data file formats developed by MDL Information Systems output_format pdb - Protein Data Bank format coordinates 3 - 3D coordinates ph 7.4 flex False binary_path obabel
Step 5: FpocketRun input PDB file Output dataset 'output_molecule_path' from step 3 output ZIP name myfpocket_run.zip output JSON name myfpocket_run.json Take tool settings: Manual Input Properties Input: min_radius 3.0 max_radius 6.0 num_spheres 35 sort_by druggability_score - this score intends to assess the likeliness of the pocket to bind a small drug like molecule binary_path fpocket
Step 6: StrCheckAddHydrogens input PDB file Output dataset 'output_molecule_path' from step 3 output PDB,PDBQT name mystr_check_add_hydrogens.pdbqt Take tool settings: Manual Input Properties Input: charges True mode auto ph 7.4 list Empty. keep_canonical_resnames True binary_path check_structure output_format pdbqt
Step 7: BabelConvert input DAT,ENT,FA,FASTA,GRO,INP,LOG,MCIF,MDL,MMCIF,MOL,MOL2,PDB,PDBQT,PNG,SDF,SMI,SMILES,TXT,XML,XTC file Output dataset 'output_path' from step 4 output ENT,FA,FASTA,GRO,INP,MCIF,MDL,MMCIF,MOL,MOL2,PDB,PDBQT,PNG,SDF,SMI,SMILES,TXT name mybabel_convert.pdbqt Take tool settings: Manual Input Properties Input: input_format pdb - Protein Data Bank format output_format pdbqt - Protein Data Bank format with charges coordinates 3 - 3D coordinates ph 7.4 flex False binary_path obabel
Step 8: FpocketFilter input ZIP file Output dataset 'output_pockets_zip' from step 5 input JSON file Output dataset 'output_summary' from step 5 output ZIP name myfpocket_filter.zip Take tool settings: Manual Input Properties Input: score [] druggability_score [] volume [800,2000]
Step 9: FpocketSelect input ZIP file Output dataset 'output_filter_pockets_zip' from step 8 output PDB name myfpocket_select.pdb output PQR name myfpocket_select.pqr Take tool settings: Manual Input Properties Input: pocket 6
Step 10: Box input PDB,PQR file Output dataset 'output_pocket_pqr' from step 9 output PDB name mybox.pdb Take tool settings: Manual Input Properties Input: offset 12.0 box_coordinates True
Step 11: AutodockVinaRun input PDBQT file Output dataset 'output_path' from step 7 input PDBQT file Output dataset 'output_structure_path' from step 6 input PDB file Output dataset 'output_pdb_path' from step 10 output PDBQT name myautodock_vina_run.pdbqt output LOG name myautodock_vina_run.log Take tool settings: Manual Input Properties Input: cpu 1 binary_path vina
Step 12: ExtractModelPdbqt input PDBQT file Output dataset 'output_pdbqt_path' from step 11 output PDBQT name myextract_model_pdbqt.pdbqt Take tool settings: Manual Input Properties Input: model 1
Step 13: BabelConvert input DAT,ENT,FA,FASTA,GRO,INP,LOG,MCIF,MDL,MMCIF,MOL,MOL2,PDB,PDBQT,PNG,SDF,SMI,SMILES,TXT,XML,XTC file Output dataset 'output_pdbqt_path' from step 12 output ENT,FA,FASTA,GRO,INP,MCIF,MDL,MMCIF,MOL,MOL2,PDB,PDBQT,PNG,SDF,SMI,SMILES,TXT name poses.pdb Take tool settings: Manual Input Properties Input: input_format pdbqt - Protein Data Bank format with charges output_format pdb - Protein Data Bank format coordinates 3 - 3D coordinates ph 7.4 flex False binary_path obabel
Step 14: CatPdb input PDB,PDBQT file Output dataset 'output_molecule_path' from step 3 input PDB,PDBQT file Output dataset 'output_path' from step 13 output PDB,PDBQT name docking1.pdb Take tool settings: Manual Input Properties Input: output_format pdb

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gbayarri

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