Figure 4.

Workflow of a Thermal Titration Molecular Dynamics (TTMD) simulation. The time-dependent conservation of the native binding mode within a protein–ligand complex of interest is monitored with a scoring function based on interaction fingerprint through a series of short molecular dynamics simulations performed at progressively increasing temperatures. The simulation is carried out until the target temperature is reached or the dissociation process is completed. A coefficient called MS is then calculated and used to rank ligands based on the persistence of their native binding mode.