The second pillar of the CLARA Testbed Infrastructure consists of software framework for modelling molecular dynamics, protein-ligand docking, machine learning as well as quantum computer simulation.
The framework will include state-of-the-art software such as Autodock Vina, AlphaFold2, Amber and AmberTools, HTMD, ParmEd, MGLTools, MDtraj, PyEMMA, Openbabel, RDKit, Schrodinger, Avogadro, Gaussian, PyTorch, MOPAC, cuQuantum, Clinica, ClinicaDL, dcm2niix, ANTs, Convert3D, FreeSurfer, FSL, ITK, Mtrix, SPM and PETPVC.