A small ligand molecule (pink chain) diffuses under thermal motion until it finds and settles into a receptor's binding pocket (blue-grey cup). Interaction forces follow a simplified Lennard-Jones-style potential balancing attraction and steric repulsion.
V(r) = 4ε[(σ/r)¹² − (σ/r)⁶] (Lennard-Jones potential per atom pair)
F_thermal = random · temperature (Brownian kick from solvent)
score = ΣV(r) over ligand–receptor atom pairs
- Temperature — strength of random thermal motion buffeting the ligand; too high prevents stable binding.
- Binding affinity — depth ε of the attractive well, representing how favorable the ligand-pocket chemistry is.
- Docking speed — overall simulation time-scale.
- Relaunch Ligand — resets the ligand to a random position outside the pocket to try docking again.
Real application: computational chemists use molecular docking scores exactly like this (simplified) one to rank candidate drug molecules by predicted binding strength to a target protein before costly lab synthesis.