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@bioexcel

BioExcel

Center of Excellence for Computational Biomolecular Research

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  1. biobb biobb Public

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

    Python 68 10

  2. gromacs-docker gromacs-docker Public

    Dockerfile for GROMACS

    Dockerfile 52 25

  3. gromacs-2022-cp2k-tutorial gromacs-2022-cp2k-tutorial Public

    Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface

    Makefile 43 9

  4. cp2K_qmmm_tutorials_for_biological_simulations cp2K_qmmm_tutorials_for_biological_simulations Public

    Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.

    Jupyter Notebook 26 8

  5. biobb_amber biobb_amber Public

    Biobb_amber is a BioBB category for AMBER MD package.

    Python 15 4

  6. biobb_structure_checking biobb_structure_checking Public

    Python 13 2

Repositories

Showing 10 of 127 repositories
  • biobb_pdb_tools Public
    bioexcel/biobb_pdb_tools's past year of commit activity
    Python 0 Apache-2.0 0 1 0 Updated Sep 14, 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.

    bioexcel/biobb_io's past year of commit activity
    Python 2 Apache-2.0 0 0 0 Updated Sep 14, 2026
  • biobb_structure_checking Public
    bioexcel/biobb_structure_checking's past year of commit activity
    Python 13 Apache-2.0 2 3 0 Updated Sep 2, 2026
  • biobb_haddock Public

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

    bioexcel/biobb_haddock's past year of commit activity
    Python 2 Apache-2.0 0 2 0 Updated Aug 12, 2026
  • utils_biobb Public
    bioexcel/utils_biobb's past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Aug 10, 2026
  • biobb_analysis Public

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

    bioexcel/biobb_analysis's past year of commit activity
    Python 4 Apache-2.0 3 1 0 Updated Aug 7, 2026
  • biobb_vs Public

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

    bioexcel/biobb_vs's past year of commit activity
    Python 2 Apache-2.0 3 0 0 Updated Aug 3, 2026
  • biobb_gromacs Public
    bioexcel/biobb_gromacs's past year of commit activity
    Python 7 Apache-2.0 3 13 0 Updated Jul 27, 2026
  • biobb Public

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

    bioexcel/biobb's past year of commit activity
    Python 68 Apache-2.0 10 2 0 Updated Jul 27, 2026
  • biobb_wf_network_analysis Public

    This workflow shows how to build and analyze dynamical correlation networks from MD simulations using biobb_dyna. It covers DCCM calculation, conversion into residue interaction networks, and graph analysis to identify dynamic bottlenecks, hubs, cooperative modules, and allosteric communication pathways.

    bioexcel/biobb_wf_network_analysis's past year of commit activity
    Jupyter Notebook 0 Apache-2.0 0 0 0 Updated Jul 27, 2026
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