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@bioexcel

BioExcel

Center of Excellence for Computational Biomolecular Research

Popular repositories

  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 48 8

  2. gromacs-docker gromacs-docker Public

    Dockerfile for GROMACS

    Dockerfile 42 18

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

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

    Makefile 25 5

  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 16 6

  5. pymdsetup pymdsetup Public

    Python 9 1

  6. biobb_structure_checking biobb_structure_checking Public

    Python 8 1

Repositories

Showing 10 of 114 repositories
  • biobb_workflows Public

    Global repository for all the BioExcel Building Blocks Workflows

    Common Workflow Language 2 2 0 0 Updated Apr 22, 2024
  • Python 0 Apache-2.0 0 0 0 Updated Apr 22, 2024
  • biobb_vs Public

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

    Python 1 Apache-2.0 2 0 0 Updated Apr 5, 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.

    Python 2 Apache-2.0 2 1 0 Updated Apr 5, 2024
  • biobb_ml Public

    Biobb_ml is the Biobb module collection to perform machine learning predictions.

    Python 1 Apache-2.0 1 0 2 Updated Apr 5, 2024
  • biobb_godmd Public

    biobb_godmd is a BioBB category for the GOdMD tool

    Python 0 Apache-2.0 0 0 0 Updated Apr 5, 2024
  • biobb_flexserv Public

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

    Python 1 Apache-2.0 0 0 0 Updated Apr 5, 2024
  • biobb_flexdyn Public

    biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.

    Python 1 Apache-2.0 0 0 0 Updated Apr 5, 2024
  • biobb_dna Public

    Biobb_dna is the Biobb module collection to perform analyses and transformations on nucleic acid trajectories and helical parameter data.

    Python 0 Apache-2.0 0 1 0 Updated Apr 5, 2024
  • Python 1 Apache-2.0 1 0 0 Updated Apr 5, 2024

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