Ultrafast algorithm for designing focused combinational arrays

A novel greedy algorithm for the design of focused combinatorial arrays is presented. The method is applicable when the objective function is decompos able to individual molecular contributions and makes use of a heuristic tha t allows the independent evaluation and ranking of candidate reagents in ea ch variation site in the combinatorial library. The algorithm is extremely fast and convergent and produces solutions that are comparable to and often better than those derived from the substantially more elaborate and comput ationally intensive stochastic sampling techniques. Typical examples of des ign objectives that are amendable to this approach include maximum similari ty to a known lead (or set of leads), maximum predicted activity according to some structure-activity or receptor binding model, containment within ce rtain molecular property bounds, and many others.