Molecular Docking Simulator

Structure-based drug discovery starts with a question docking software answers thousands of times per screen: given a protein's binding pocket, which orientation and position of a candidate molecule binds most tightly? This simulator renders a real binding-pocket geometry — residues colored by hydrophobic, polar, acidic and basic character — and a rigid small-molecule ligand carrying its own hydrophobic core, polar carbonyls and a protonated amine. A Metropolis Monte Carlo / simulated-annealing search repeatedly proposes small translations and rotations of the ligand, scores each candidate pose with a Lennard-Jones plus Coulomb energy function summed over every ligand-residue atom pair, and accepts or rejects the move according to the physical Metropolis criterion. Watch the ligand explore broadly at high temperature and settle into a low-energy pose as the search anneals, with live readouts for the current score, the best pose found so far, and the trial acceptance rate.