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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.

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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