Repositories list

• 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

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  Apache License 2.0

  •0•0•1•0•Updated Sep 8, 2025Sep 8, 2025

• biobb_analysis

  Public
  Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.

  Python

  •

  Apache License 2.0

  •3•4•0•0•Updated Sep 8, 2025Sep 8, 2025

• biobb_mem

  Public
  Python

  •

  Apache License 2.0

  •0•0•3•0•Updated Sep 8, 2025Sep 8, 2025

• biobb_haddock

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

  Python

  •

  Apache License 2.0

  •0•2•2•0•Updated Sep 5, 2025Sep 5, 2025

• biobb_pdb_tools

  Public
  Python

  •

  Apache License 2.0

  •0•0•1•0•Updated Sep 5, 2025Sep 5, 2025

• biobb_common

  Public
  Biobb_common is the base package required to use the biobb packages.

  Python

  •

  Apache License 2.0

  •1•0•3•0•Updated Sep 4, 2025Sep 4, 2025

• 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 Sep 4, 2025Sep 4, 2025

• 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 Sep 3, 2025Sep 3, 2025

• utils_biobb

  Public
  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Aug 25, 2025Aug 25, 2025

• biobb_adapters

  Public
  Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.

  Common Workflow Language

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  Apache License 2.0

  •5•0•6•0•Updated Aug 19, 2025Aug 19, 2025

• biobb

  Public
  Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.

  Python

  •

  Apache License 2.0

  •9•60•1•0•Updated Aug 12, 2025Aug 12, 2025

• biobb_ml

  Public
  Biobb_ml is the Biobb module collection to perform machine learning predictions.

  Python

  •

  Apache License 2.0

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

• 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

  •1•2•0•0•Updated Aug 11, 2025Aug 11, 2025

• biobb_flexdyn

  Public
  biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.

  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_pmx

  Public
  Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.

  Python

  •

  Apache License 2.0

  •0•3•2•0•Updated Aug 6, 2025Aug 6, 2025

• 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 Aug 6, 2025Aug 6, 2025

• 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, removing water molecules or ligands, or renumbering or sorting atoms or residues.

  Python

  •

  Apache License 2.0

  •3•2•1•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_vs

  Public
  Biobb_vs is the Biobb module collection to perform virtual screening studies.

  Python

  •

  Apache License 2.0

  •2•1•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_model

  Public
  Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.

  Python

  •

  Apache License 2.0

  •1•1•2•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_godmd

  Public
  biobb_godmd is a BioBB category for the GOdMD tool

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_flexserv

  Public
  Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.

  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_cp2k

  Public
  Python

  •

  Apache License 2.0

  •1•1•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_dna

  Public
  Biobb_dna is the Biobb module collection to perform analyses and transformations on nucleic acid trajectories and helical parameter data.

  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_cmip

  Public
  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_chemistry

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

  Python

  •

  Apache License 2.0

  •2•5•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_amber

  Public
  Biobb_amber is a BioBB category for AMBER MD package.

  Python

  •

  Apache License 2.0

  •3•13•2•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_gromacs

  Public
  Python

  •

  Apache License 2.0

  •1•5•11•0•Updated Aug 6, 2025Aug 6, 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

  •

  Apache License 2.0

  •1•3•0•0•Updated Aug 6, 2025Aug 6, 2025

• biobb_workflows

  Public
  Global repository for all the BioExcel Building Blocks Workflows

  Common Workflow Language

  •3•5•0•0•Updated Aug 5, 2025Aug 5, 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

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025