Accurate description of protein-ligand interactions is one of thecentral problems in molecular biology with applications in medicine andpharmacology (e.g. drug design). In this talk a critical review of thecurrent methods employed in such studies is given and some applications tospecific protein-ligand pairs are presented. Feasibility of a docking + MDsimulations approach is demonstrated for binding of organic cations to thegramicidin channel. These methods are then applied to more realistic casesinvolving binding of certain toxins to potassium channels, which areconsidered as drug leads.