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41:5272– 86 Hansson T, Marelius J, Aqvist J. 1998. Ligand binding affinity prediction by linear interaction energy methods. J. -Aided Molec. Des. 12:27–35 Marelius J, GraffnerNordberg M, Hansson T, Hallberg A, Aqvist J. 1998. Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases. J. -Aided Molec. Des. 12:119–31 Carlson HA, Masukawa KM, McCammon JA. 1999. Method for including the dynamic fluctuations of a protein in computer-aided drug design.
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However, progress has been made in developing new algorithms to accelerate these calculations, in employing implicit rather than explicit solvent models to facilitate solute conformational samplings, and in introducing approximate methods to screen many derivatives of a drug lead more efficiently. Here, we briefly review some earlier work and then discuss various encouraging recent developments. FREE ENERGY CALCULATIONS In 1984 (2), the thermodynamic cycle-perturbation method was introduced to help compare the binding affinity of a group of similar inhibitors.