BioExcel
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gromacs-2022-cp2k-tutorial
gromacs-2022-cp2k-tutorial PublicSample inputs and tutorial for GROMACS-2022/CP2K QMMM interface
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cp2K_qmmm_tutorials_for_biological_simulations
cp2K_qmmm_tutorials_for_biological_simulations PublicSeveral QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
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Repositories
- utils_biobb Public
- biobb_haddock Public
biobb_haddock is the Biobb module collection to compute information-driven flexible protein-protein docking.
- biobb_gromacs Public
- biobb Public
Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.
- 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.
- biobb_mem Public
- 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.
- biobb_pytorch Public
Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.
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