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  1. Protein-Ligand-Interaction-Analysis Protein-Ligand-Interaction-Analysis Public

    Analysis on the number of non-hydrogen atomic contacts between a ligand and each of specified residues on the protein following molecular docking of multiple ligands to a protein structure.

    Python 3 2

  2. Simulated-Annealing Simulated-Annealing Public

    The simulated annealing algorithm that minimizes a cost function, which indicates the degree of matching between the force field (FF) and density-functional theory (DFT).

    Python 1

  3. Molecular-Dynamics-Simulations Molecular-Dynamics-Simulations Public

    Bash shell scripts that process GROMACS files for automating a series of molecular-dynamics (MD) simulations on NERSC supercomputer.

    Shell 1

  4. Protein-Ligand-Docking-Score-Ranking Protein-Ligand-Docking-Score-Ranking Public

    Ranking of all the ligands in molecular docking by their AutoDock Vina scores, an approximation to their free energy of binding to the protein.

    Python