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    121 repositories

    • biobb_gromacs

      Public
      Python
      •
      Apache License 2.0
      •1•5•12•0•Updated Jul 31, 2025Jul 31, 2025

    • biobb_mem

      Public
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Jul 31, 2025Jul 31, 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
      •
      Apache License 2.0
      •3•1•0•0•Updated Jul 31, 2025Jul 31, 2025

    • biobb_adapters

      Public
      Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.
      Common Workflow Language
      •
      Apache License 2.0
      •5•1•4•0•Updated Jul 31, 2025Jul 31, 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•59•0•0•Updated Jul 31, 2025Jul 31, 2025

    • biobb_workflows

      Public
      Global repository for all the BioExcel Building Blocks Workflows
      Common Workflow Language
      •3•5•0•0•Updated Jul 31, 2025Jul 31, 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
      •
      Apache License 2.0
      •2•1•0•1•Updated Jul 31, 2025Jul 31, 2025

    • biobb_hpc_workflows

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 31, 2025Jul 31, 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 Jul 30, 2025Jul 30, 2025

    • biobb_structure_checking

      Public
      Python
      •
      Apache License 2.0
      •1•11•3•1•Updated Jul 16, 2025Jul 16, 2025

    • 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 Jul 15, 2025Jul 15, 2025

    • biobb_pdb_tools

      Public
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Jun 30, 2025Jun 30, 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 30, 2025Jun 30, 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 30, 2025Jun 30, 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 Jun 25, 2025Jun 25, 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•2•0•Updated Jun 25, 2025Jun 25, 2025

    • utils_biobb

      Public
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 25, 2025Jun 25, 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 25, 2025Jun 25, 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 20, 2025Jun 20, 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 20, 2025Jun 20, 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 20, 2025Jun 20, 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 20, 2025Jun 20, 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 20, 2025Jun 20, 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 20, 2025Jun 20, 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 19, 2025Jun 19, 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 19, 2025Jun 19, 2025

    • biobb_cp2k

      Public
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Jun 19, 2025Jun 19, 2025

    • biobb_cmip

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 19, 2025Jun 19, 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 19, 2025Jun 19, 2025

    • biobb_amber

      Public
      Biobb_amber is a BioBB category for AMBER MD package.
      Python
      •
      Apache License 2.0
      •3•13•3•0•Updated Jun 19, 2025Jun 19, 2025