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    122 repositories

    • biobb_workflows

      Public
      Global repository for all the BioExcel Building Blocks Workflows
      Common Workflow Language
      •4•8•0•0•Updated Feb 20, 2026Feb 20, 2026

    • biobb_wf_haddock

      Public
      This tutorials aim to illustrate the process of protein-protein docking, step by step, using HADDOCK with the BioExcel Building Blocks library (biobb).
      Jupyter Notebook
      •
      Apache License 2.0
      •1•3•1•0•Updated Feb 20, 2026Feb 20, 2026

    • biobb_pdb_tools

      Public
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Feb 17, 2026Feb 17, 2026

    • utils_biobb

      Public
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • 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 B…
      HTML
      •
      Apache License 2.0
      •0•1•0•0•Updated Feb 17, 2026Feb 17, 2026

    • 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
      •
      Apache License 2.0
      •1•3•0•0•Updated Feb 17, 2026Feb 17, 2026

    • 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 …
      HTML
      •
      Apache License 2.0
      •0•2•0•0•Updated Feb 17, 2026Feb 17, 2026

    • biobb_gromacs

      Public
      Python
      •
      Apache License 2.0
      •2•5•12•0•Updated Feb 17, 2026Feb 17, 2026

    • biobb_cmip

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • 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
      •
      Apache License 2.0
      •5•6•0•0•Updated Feb 13, 2026Feb 13, 2026

    • 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 BioExce…
      HTML
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      Apache License 2.0
      •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • 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 …
      HTML
      •
      Apache License 2.0
      •1•2•0•0•Updated Feb 13, 2026Feb 13, 2026

    • 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
      •
      Apache License 2.0
      •2•1•0•1•Updated Feb 13, 2026Feb 13, 2026

    • 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 B…
      HTML
      •
      Apache License 2.0
      •6•8•0•0•Updated Feb 13, 2026Feb 13, 2026

    • biobb_wf_mem

      Public
      This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb).
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • 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 (b…
      HTML
      •
      Apache License 2.0
      •4•4•0•0•Updated Feb 13, 2026Feb 13, 2026

    • biobb_wf_autoencoder

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •1•0•0•1•Updated Feb 13, 2026Feb 13, 2026

    • 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 (b…
      HTML
      •
      Apache License 2.0
      •3•1•0•0•Updated Feb 13, 2026Feb 13, 2026

    • 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, usi…
      HTML
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      Apache License 2.0
      •1•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • biobb_common

      Public
      Biobb_common is the base package required to use the biobb packages.
      Python
      •
      Apache License 2.0
      •1•0•2•0•Updated Feb 12, 2026Feb 12, 2026

    • biobb_mem

      Public
      Python
      •
      Apache License 2.0
      •0•0•3•0•Updated Feb 5, 2026Feb 5, 2026

    • biobb_pytorch

      Public
      Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Feb 4, 2026Feb 4, 2026

    • biobb_io

      Public
      Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Feb 4, 2026Feb 4, 2026

    • 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 …
      HTML
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      Apache License 2.0
      •1•1•0•0•Updated Jan 29, 2026Jan 29, 2026

    • gromacs-2022-cp2k-tutorial

      Public
      Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface
      Makefile
      •9•42•0•0•Updated Jan 29, 2026Jan 29, 2026

    • biobb_structure_utils

      Public
      Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain…
      Python
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      Apache License 2.0
      •3•2•1•0•Updated Jan 23, 2026Jan 23, 2026

    • biobb_template

      Public
      Biobb_template is a complete code template to promote and facilitate the creation of new Biobbs by the community.
      Python
      •
      Apache License 2.0
      •2•2•0•0•Updated Dec 22, 2025Dec 22, 2025

    • biobb_pmx

      Public
      Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
      Python
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      Apache License 2.0
      •0•3•2•0•Updated Dec 22, 2025Dec 22, 2025

    • biobb_vs

      Public
      Biobb_vs is the Biobb module collection to perform virtual screening studies.
      Python
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      Apache License 2.0
      •2•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • biobb_model

      Public
      Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.
      Python
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      Apache License 2.0
      •1•1•2•0•Updated Dec 22, 2025Dec 22, 2025