*2.2. MELD*×*MD Simulations Balance Exploration and Exploitation of the Binding Energy Landscape*

Figure 3 provides a visual outlook on the binding process explored by the MELD×MD replica exchange procedure in terms of the relative position of the peptide with respect the protein and the peptide's intrinsic conformational preferences. At high replica indexes, the force constants for the restraints are set to zero and the temperature is high (see methods). In these conditions, the peptide samples conformations far away from the active site, distributed uniformly around the protein. During the binding process, the MDM2 flexibility allows for the opening and closing of the binding cavity (see right panel in Figure A5). As the replica index decreases, the temperature decreases and the biasing restraints towards the protein become active, producing a frustrated energy landscape. Under these conditions, the peptide samples conformations on the surface of the protein, identifying early on the MDM2 hydrophobic pocket as the most likely region for binding. Sampling is concentrated in the binding pocket at the lowest replica. Thus, at the highest replica, the protocol favors full exploration of the energy landscape, while, at the lowest replica, it favors full exploitation by sampling around a particular binding region near the protein. The nature of MELD×MD enhances binding/unbinding events by allowing replicas to explore different Hamiltonian and temperature conditions, leading to a different balance of exploration and exploitation [27,28].
