Flexible alignment of small molecules

A method is presented for flexibly aligning small molecules. The method acc epts a collection of small molecules with 3D coordinates as input and compu tes a collection of alignments. Each alignment is given a score, which quan tifies the quality of the alignment both in terms of internal strain and ov erlap of molecular features. The results of several computational experimen ts on pairs of compounds with known binding conformations are used to syste matically and objectively tune the parameters for the method. The results i ndicate the method's utility for the elucidation of pharmacophores and comp arative field analysis.