Repositories list

• biobb_haddock

  Public
  biobb_haddock is the Biobb module collection to compute information-driven flexible protein-protein docking.

  Python

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_pdb_tools

  Public
  Python

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_chemistry

  Public
  Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.

  Python

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  Apache License 2.0

  •2•5•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_workflows

  Public
  Global repository for all the BioExcel Building Blocks Workflows

  Common Workflow Language

  •2•4•0•0•Updated Mar 12, 2025Mar 12, 2025

• utils_biobb

  Public
  Python

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  Apache License 2.0

  •1•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_virtual-screening

  Public
  This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •4•5•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_structure_checking

  Public
  This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_protein-complex_md_setup

  Public
  This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •6•5•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_pmx_tutorial

  Public
  This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •1•2•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_md_setup_remote

  Public
  Jupyter Notebook

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_md_setup_membrane

  Public
  Jupyter Notebook

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_md_setup_api

  Public
  This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, accessing the BioExcel Building Blocks library (biobb) through the REST API.

  HTML

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  Apache License 2.0

  •1•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_md_setup

  Public
  This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •4•4•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_ligand_parameterization

  Public
  This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •2•1•0•1•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_godmd

  Public
  This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •1•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_flexserv

  Public
  This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •1•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_flexdyn

  Public
  This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •0•1•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_dna_helparms

  Public
  This tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •1•1•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_cwl_tutorial

  Public
  HTML

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  Apache License 2.0

  •2•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_command-line

  Public
  This tutorial aims to illustrate the process of building up a command-line workflow using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_cmip

  Public
  This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb).

  HTML

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_autoencoder

  Public
  Jupyter Notebook

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  Apache License 2.0

  •1•0•0•1•Updated Mar 12, 2025Mar 12, 2025

• biobb_wf_amber

  Public
  This tutorials aim to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.

  HTML

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  Apache License 2.0

  •3•1•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_REST_API_documentation

  Public
  This tutorial explains how to execute the different endpoints of the BioBB REST API.

  Jupyter Notebook

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• zip_container

  Public
  Dockerfile

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• pmx_container

  Public
  Dockerfile

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• obabel_singularity

  Public
  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• ambertools_singularity

  Public
  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• acpype_container

  Public
  Dockerfile

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  Apache License 2.0

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• biobb_websites

  Public
  0•0•1•0•Updated Mar 12, 2025Mar 12, 2025