All Published Workflows

5 workflows that have been reviewed and published

cwl-protein-ligand-complex-md-setup-tutorial
Show Details View Workflow
CWL Protein Ligand Complex MD Setup tutorial using Biobb
public

public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
CWL Protein-ligand complex biobb_structure_utils biobb_analysis biobb_chemistry biobb_gromacs biobb_model genion Gromacs editconf gmx energy Protein interactions
Free
18
protein-ligand-docking-fpocket
Show Details View Workflow
Protein-ligand docking (fpocket)
public

public

This workflow performs the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).
CWL PDB Protein-ligand complex Molecular docking Protein-ligand interaction report biobb_structure_utils biobb_vs AutoDock Vina Fpocket Open Babel Molecular modelling
Free
5
gromacs-dctmd-main
Show Details View Workflow
gromacs-dctmd free energy calculation
public

public

Perform an ensemble of targeted MD simulations of a user-specified size using the GROMACS PULL code and calculate dcTMD free ...
Protein-ligand complex Simulation analysis Protein-ligand interaction report gromacs_mpi ChemicalToolbox Galaxy Gromacs WorkflowHub Molecular dynamics
Free
gromacs-mmgbsa-main
Show Details View Workflow
GROMACS MMGBSA free energy calculation
public

public

Perform an ensemble of MD simulations of a user-specified size using GROMACS, and calculate MMGBSA free energies using AmberT...
Protein-ligand complex Modelling and simulation Protein-ligand interaction report gromacs_mpi AmberTools Galaxy Gromacs WorkflowHub Biomolecular simulation
Free
fragment-based-docking-scoring-main
Show Details View Workflow
Fragment-based virtual screening with docking and pose scoring
public

public

Dock a compound library against a target protein with rDock and validate the poses generated against a reference fragment usi...
SDF Protein-ligand complex Virtual screening Position-specific scoring matrix Deep Docking Galaxy Open Babel RDKit SuCOS WorkflowHub Protein binding sites
Free