All Published Workflows

5 workflows that have been reviewed and published

jupyter-notebook-protein-conformational-ensembles
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Jupyter Notebook Protein conformational ensembles generation
public

public

Protein Conformational ensembles generation This tutorial aims to illustrate the process of generating protein conformation...
JSON PDB Clustering biobb_structure_utils biobb_analysis biobb_flexdyn biobb_flexserv biobb_gromacs biobb_io concoord nolb Gromacs IMOD NGLview NMA Pandas ProDy CPPTRAJ biobb-analysis biobb-flexdyn biobb-flexserv biobb-gromacs biobb-io biobb-structure-utils ipython ipywidgets numpy plotly simpletraj Protein structure analysis
Free
78
galaxy-protein-md-setup-tutorial
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Galaxy Protein MD Setup tutorial
public

public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
PDB Protein features Simulation analysis PDB ID genion BioBB-Wfs BioExcel Building Blocks tutorials: Protein MD Setup (Gromacs Version) Galaxy Gromacs NVT WorkflowHub Protein properties
Free
cwl-amber-protein-md-setup-tutorial
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CWL Amber Protein MD Setup tutorial
public

public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
PDB Protein complex Modelling and simulation Molecular simulation data biobb_structure_utils biobb_amber biobb_analysis biobb_chemistry CPPTRAJ Biomolecular simulation
Free
14
protein-ligand-docking-fpocket
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Protein-ligand docking (fpocket)
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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
protein-ligand-complex-parameterization-main
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protein ligand complex parameterization
public

public

Parameterizes an input protein (PDB) and ligand (SDF) file prior to molecular dynamics simulation with GROMACS. This is a sim...
PDB Protein accession Protein architecture analysis Protein-ligand complex gromacs_mpi AmberTools Galaxy Gromacs Open Babel RDKit WorkflowHub Biomolecular simulation
Free