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Computational methods to predict binding free energy in ligand-receptor complexes.

Most biological processes depend on the ability of molecules to bind and discriminate between one another. The ability to form noncovalent complexes is ubiquitous in reactions among biological macromolecules. This association is essential for many functions,1 eg., catalysis, transport, or signal transduction. Structural information gathered over the past three decades has helped us understand many complexes at the molecular level providing a detailed description of the interaction between a receptor and its ligands. Binding can be remarkably sensitive to even small differences in structure. A quantitative knowledge of the binding process is therefore essential to understanding molecular recognition. Such a quantitative knowledge requires (1) a detailed understanding of the physical forces involved in the interaction and (2) a measure of the extent to which these forces contribute to the overall reaction procedure. Thermodynamics governs the basic physical principles of molecular recognition. Therefore, the fundamentals processes involved in the binding of two or more molecules are similar to those for the folding of proteins. Binding, however, should be a simpler problem compared to folding as a smaller number (10-30) of amino acids, mostly in the active site, are involved. The affinity of two molecules that form a noncovalent complex is described by the change in enthalpy and entropy of the system. The system consists of the molecules and solvent (before complex formation) and the complex and solvent (see Figure 1). In general,