All Published Workflows

18 workflows that have been reviewed and published

ddamsproteomics
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Quantitative shotgun MS proteomics
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public

Quantitative shotgun MS proteomics as done in Lehtio lab The pipeline is built using Nextflow , a workflow...
msgf_plus Spectra Nextflow OpenMS Quant Protein expression Protein interactions Protein structure analysis
Free
22
python-mutation-free-energy-calculations-using-bio
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Python Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)
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public

Mutation Free Energy Calculations using BioExcel Building Blocks (biobb) Based on the official pmx tutorial . This tu...
biobb_common biobb_gromacs biobb_pmx Gromacs biobb-analysis biobb-common biobb-gromacs biobb-pmx DNA mutation Protein interactions
Free
1
galaxy-protein-ligand-complex-md-setup
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Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)
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public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
PDB ID Ligand-binding site prediction PDB ID genion ACPYPE BioBB-Wfs BioExcel Building Blocks tutorials: Protein MD Setup (Gromacs Version) Galaxy Gromacs NVT Open Babel WorkflowHub Protein interactions
Free
python-cns-xplor-md-automatic-ligand-parameterizat
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Python CNS/XPLOR MD Automatic Ligand Parameterization tutorial using Biobb
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public

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb) This tutorial aims to illustrate the proces...
biobb_chemistry biobb_common ACPYPE Open Babel biobb-chemistry biobb-common Protein interactions
Free
2
python-amber-automatic-ligand-parameterization-tut
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Python Amber Automatic Ligand Parameterization tutorial using BioExcel Building Blocks (biobb)
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public

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb) This tutorial aims to illustrate the...
biobb_chemistry biobb_common Open Babel biobb-chemistry biobb-common Protein interactions
Free
3
cwl-protein-md-setup-tutorial-with-mutations
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CWL Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
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public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
CWL biobb_structure_utils biobb_analysis biobb_chemistry biobb_gromacs biobb_model genion Gromacs editconf gmx energy DNA mutation Protein interactions
Free
17
python-protein-md-analysis-tutorial
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Python Protein MD Analysis tutorial using biobb
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public

This workflow computes a set of Quality Control (QC) analyses on top of an uploaded MD trajectory. QC analyses include positi...
JSON biobb_analysis biobb_common Biopython Gromacs CPPTRAJ biobb-analysis biobb-common pdbparser Protein interactions
Free
1
python-abc-md-setup-tutorial
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Python ABC MD Setup tutorial using BioExcel Building Blocks (biobb)
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public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
biobb_amber biobb_analysis biobb_common CPPTRAJ biobb-amber biobb-analysis biobb-common Protein interactions
Free
1
python-amber-protein-md-setup-tutorial
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Python Amber Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
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public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
biobb_structure_utils biobb_amber biobb_analysis biobb_chemistry biobb_common CPPTRAJ biobb-amber biobb-analysis biobb-chemistry biobb-common biobb-structure-utils Protein interactions
Free
1
python-gmx-automatic-ligand-parameterization-tutor
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Python GMX Automatic Ligand Parameterization tutorial using Biobb
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public

This tutorial aims to illustrate the process of ligand parameterization for a small molecule , step by step, using the Bi...
biobb_chemistry biobb_common ACPYPE Open Babel biobb-chemistry biobb-common Protein interactions
Free
1
python-protein-md-setup-tutorial
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Python Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
public

public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
biobb_structure_utils biobb_analysis biobb_chemistry biobb_common biobb_gromacs biobb_model genion Gromacs editconf gmx energy biobb-analysis biobb-chemistry biobb-common biobb-gromacs biobb-model biobb-structure-utils Protein interactions
Free
1
cwl-abc-md-setup-tutorial
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CWL AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)
public

public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
CWL biobb_amber biobb_analysis CPPTRAJ Protein interactions
Free
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