Repositories list

• biobb_gromacs

  Public
  Python

  •

  Apache License 2.0

  •1•5•13•0•Updated Jun 11, 2025Jun 11, 2025

• biobb_pdb_tools

  Public
  Python

  •

  Apache License 2.0

  •0•0•1•0•Updated Jun 11, 2025Jun 11, 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 Jun 11, 2025Jun 11, 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 Jun 11, 2025Jun 11, 2025

• biobb_md

  Public
  Biobb_md is the Biobb module collection to perform molecular dynamics simulations.

  Python

  •

  Apache License 2.0

  •3•7•0•0•Updated Jun 11, 2025Jun 11, 2025

• biobb_common

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

  Python

  •

  Apache License 2.0

  •1•1•3•0•Updated Jun 11, 2025Jun 11, 2025

• biobb_godmd

  Public
  biobb_godmd is a BioBB category for the GOdMD tool

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 10, 2025Jun 10, 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 Jun 10, 2025Jun 10, 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•1•0•0•Updated Jun 8, 2025Jun 8, 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 Jun 6, 2025Jun 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 Jun 6, 2025Jun 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 Jun 6, 2025Jun 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 Jun 6, 2025Jun 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 Jun 6, 2025Jun 6, 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 Jun 6, 2025Jun 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 Jun 6, 2025Jun 6, 2025

• biobb_cp2k

  Public
  Python

  •

  Apache License 2.0

  •1•1•0•0•Updated Jun 6, 2025Jun 6, 2025

• biobb_cmip

  Public
  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 6, 2025Jun 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 Jun 6, 2025Jun 6, 2025

• biobb_amber

  Public
  Biobb_amber is a BioBB category for AMBER MD package.

  Python

  •

  Apache License 2.0

  •3•11•2•0•Updated Jun 6, 2025Jun 6, 2025

• biobb_structure_checking

  Public
  Python

  •

  Apache License 2.0

  •1•11•2•1•Updated Jun 5, 2025Jun 5, 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•1•5•0•Updated May 9, 2025May 9, 2025

• biobb_workflows

  Public
  Global repository for all the BioExcel Building Blocks Workflows

  Common Workflow Language

  •3•5•0•0•Updated Mar 12, 2025Mar 12, 2025

• utils_biobb

  Public
  Python

  •

  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

  •

  Apache License 2.0

  •5•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

  •

  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

  •

  Apache License 2.0

  •6•7•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

  •

  Apache License 2.0

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

• biobb_wf_md_setup_remote

  Public
  Jupyter Notebook

  •

  Apache License 2.0

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

• biobb_wf_md_setup_membrane

  Public
  Jupyter Notebook

  •

  Apache License 2.0

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