Coarse-grained lattice model for investigating the role of cooperativity in molecular recognition

Equilibrium aspects of the molecular recognition of rigid biomolecules are investigated using coarse-grained lattice models. The analysis is carried out in two stages. First, an ensemble of probe molecules is designed with respect to the target biomolecule. The recognition ability of the probe ensemble is then investigated by calculating the free energy of association. The influence of cooperative and anticooperative effects accompanying the association of the target and probe molecules is studied. Numerical findings are presented and compared to analytical results which can be obtained in the limit of dominating cooperativity and in the mean-field formulation of the models.