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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 61 9

  2. gromacs-docker gromacs-docker Public

    Dockerfile for GROMACS

    Dockerfile 51 24

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

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

    Makefile 37 8

  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 22 8

  5. biobb_amber biobb_amber Public

    Biobb_amber is a BioBB category for AMBER MD package.

    Python 13 3

  6. biobb_structure_checking biobb_structure_checking Public

    Python 12 1

Repositories

Showing 10 of 121 repositories
  • biobb_pytorch Public

    Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.

    bioexcel/biobb_pytorch’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Sep 24, 2025
  • bioexcel/biobb_hpc_workflows’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Sep 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.

    bioexcel/biobb’s past year of commit activity
    Python 61 Apache-2.0 9 1 0 Updated Sep 18, 2025
  • biobb_adapters Public

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

    bioexcel/biobb_adapters’s past year of commit activity
    Common Workflow Language 0 Apache-2.0 5 6 0 Updated Sep 18, 2025
  • biobb_flexserv Public

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

    bioexcel/biobb_flexserv’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Sep 18, 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).

    bioexcel/biobb_wf_haddock’s past year of commit activity
    Jupyter Notebook 3 Apache-2.0 1 1 0 Updated Sep 16, 2025
  • bioexcel/biobb_structure_checking’s past year of commit activity
    Python 12 Apache-2.0 1 3 1 Updated Sep 15, 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).

    bioexcel/biobb_wf_mem’s past year of commit activity
    Jupyter Notebook 0 Apache-2.0 0 0 0 Updated Sep 8, 2025
  • 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 0 0 Updated Sep 8, 2025
  • biobb_mem Public
    bioexcel/biobb_mem’s past year of commit activity
    Python 0 Apache-2.0 0 3 0 Updated Sep 8, 2025

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