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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 54 8

  2. gromacs-docker gromacs-docker Public

    Dockerfile for GROMACS

    Dockerfile 44 19

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

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

    Makefile 33 6

  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 21 7

  5. biobb_structure_checking biobb_structure_checking Public

    Python 11 1

  6. biobb_amber biobb_amber Public

    Biobb_amber is a BioBB category for AMBER MD package.

    Python 11 3

Repositories

Showing 10 of 118 repositories
  • biobb_mem Public
    bioexcel/biobb_mem’s past year of commit activity
    Python 0 Apache-2.0 0 2 0 Updated Dec 16, 2024
  • 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 Dec 10, 2024
  • biobb_workflows Public

    Global repository for all the BioExcel Building Blocks Workflows

    bioexcel/biobb_workflows’s past year of commit activity
    Common Workflow Language 4 2 0 0 Updated Nov 29, 2024
  • biobb_model Public

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

    bioexcel/biobb_model’s past year of commit activity
    Python 1 Apache-2.0 1 2 0 Updated Nov 21, 2024
  • 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 1 Apache-2.0 2 0 0 Updated Nov 21, 2024
  • 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.

    bioexcel/biobb_structure_utils’s past year of commit activity
    Python 2 Apache-2.0 3 1 1 Updated Nov 21, 2024
  • 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 Nov 21, 2024
  • biobb_pmx Public

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

    bioexcel/biobb_pmx’s past year of commit activity
    Python 2 Apache-2.0 0 2 0 Updated Nov 20, 2024
  • biobb_pdb_tools Public
    bioexcel/biobb_pdb_tools’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Nov 20, 2024
  • 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 0 Apache-2.0 0 0 0 Updated Nov 20, 2024
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