Scoring functions: a view from the bench.

Computational approaches to drug design are presently hindered by the complexity of the physical chemistry which underlies weak, non-covalent interactions between protein targets and small molecule ligands. Although a number of programs are now available for the design of novel potential ligands, it remains a key problem to rank these rapidly and reliably by estimated binding affinity. Such a step is necessary to select only the most promising candidates for synthesis and experimental characterisation. To calculate ligand affinity quickly and reliably is an extremely difficult problem, but it may well prove possible to estimate sufficiently accurately given an appropriate set of parameters to 'score' individual protein-ligand interactions. Improvements in the situation will require a wider set of thermodynamically characterised systems than is currently available.