All Published Workflows

18 workflows that have been reviewed and published

rindti
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RINDTI: Simplifying Drug-Target Interaction Prediction with Protein Residue Interaction Networks
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This repository aims to simplify the drug-target interaction prediction process which is based on protein residue interaction...
Target-Decoy Pandas RDKit Snakemake joblib numpy sklearn torch torch-geometric tqdm utils esm Protein interaction experiment
Free
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cutandrun
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Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
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nf-core/cutandrun is a best-practice bioinformatic analysis pipeline for CUT&RUN, CUT&Tag, and TIPseq experimental protoco...
bigWig macs2 preseq tabix ucsc-bedclip PCAtools bedGraphToBigWig BEDTools Bowtie 2 DeepTools FastQC GFFutils MultiQC Nextflow Picard SAMtools PyYAML Trim_Galore Protein interaction experiment
Free
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cwl-gmx-automatic-ligand-parameterization-tutorial
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GMX Automatic Ligand Parameterization tutorial using Biobb
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This tutorial aims to illustrate the process of ligand parameterization for a small molecule , step by step, using the Bi...
CWL Ligand-binding site prediction ACPYPE Open Babel Protein interaction experiment
Free
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galaxy-amber-protein-ligand-complex-md-setup-tutor
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Galaxy Amber Protein Ligand Complex MD Setup tutorial
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Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
AMBER BioBB-Wfs BioExcel Building Blocks tutorials: Protein-Ligand Complex MD Setup (Amber Version) Galaxy Gromacs WorkflowHub Protein interaction experiment
Free
galaxy-amber-protein-md-setup-tutorial
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Galaxy Amber Protein MD Setup tutorial
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Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
AMBER BioBB-Wfs BioExcel Building Blocks tutorials: Protein MD Setup (Amber Version) Galaxy Gromacs NVT WorkflowHub Protein interaction experiment
Free
galaxy-protein-ligand-docking-tutorial-fpocket
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Protein-ligand Docking tutorial (Fpocket) using BioExcel Building Blocks
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Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb) This tutorials aim to illustrate the process of pro...
SDF AutoDock Vina BioBB-Wfs BioExcel Building Blocks tutorials: Protein-ligand Docking CAT Fpocket Galaxy Open Babel WorkflowHub Protein interaction experiment
Free
galaxy-gmx-automatic-ligand-parameterization-tutor
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Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)
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This tutorial aims to illustrate the process of ligand parameterization for a small molecule , step by step, using the Bi...
Protein name Ligand-binding site prediction PDB ID ACPYPE BioBB-Wfs BioExcel Building Blocks tutorials: Automatic Ligand parameterization Galaxy Gromacs Open Babel WorkflowHub Protein interaction experiment
Free
python-gmx-opls-aa-automatic-ligand-parameterizati
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Python GMX OPLS/AA Automatic Ligand Parameterization tutorial using Biobb
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Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb) This tutorial aims to illustrate the...
biobb_chemistry biobb_common ACPYPE Open Babel biobb-chemistry biobb-common Protein interaction experiment
Free
4
python-amber-protein-ligand-complex-md-setup-tutor
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Python Amber Protein Ligand Complex MD Setup tutorial using Biobb
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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 interaction experiment
Free
1
python-protein-ligand-docking-tutorial-fpocket
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Python Protein-ligand Docking tutorial (Fpocket) using BioExcel Building Blocks (biobb)
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public

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb) This tutorials aim to illustrate the process of pro...
Protein-ligand docking biobb_structure_utils biobb_chemistry biobb_common biobb_vs AutoDock Vina Fpocket Open Babel biobb-chemistry biobb-common biobb-structure-utils biobb-vs Protein interaction experiment
Free
1
python-protein-ligand-complex-md-setup-tutorial
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Python Protein Ligand Complex MD Setup tutorial using 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...
Protein-ligand complex 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 interaction experiment
Free
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jupyter-notebook-amber-protein-ligand-complex-md-s
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Jupyter Notebook Amber Protein Ligand Complex MD Setup tutorial using Biobb
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Based on the official GROMACS tutorial . This tutorials aim to illustrate the process of setting up a simulation system c...
Protein-ligand complex Protein-ligand docking biobb_structure_utils biobb_amber biobb_analysis biobb_chemistry biobb_io NGLview Open Babel CPPTRAJ biobb-amber biobb-analysis biobb-chemistry biobb-io biobb-structure-utils ipywidgets plotly Protein interaction experiment
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