一个药物分子经过物理或电场作用形成三维功能结构从而引起分子的药理活动。一般而言，药效基因是指原子和功能基团的结合，使得药物以特定方式与靶蛋白作用并显示药物活性。人们已经发展了很多研究药物先导物和其针对特定靶子的可测量活性的方法，使得研究者能够从一系列结构活性关系中得到其药效基因。这些方法中最成熟的是用复杂的统计计算机模型和三维数据库查询，识别和设计具有相近或相同药效基因的复合物或整个文库。药效基因的识别不仅在药物识别和设计中有用，而且对先导物优化药效减少毒性也大有用途。这是因为一旦知道药效基因，药物化学家就可以修饰它，在保持药效的基础上减少毒性。

The three-dimensional “functional shape” formed by the steric (physical) and electric fields of a drug molecule that cause the molecule’s pharmacological activity. Typically, pharmacophore refers to the combination of atoms and functional groups (together with their three-dimensional positions), that together allow a drug to interact with its target protein in a specific manner and exhibit its pharmacological activity. Numerous approaches for studying drug leads and their measurable activity against a particular target have been developed, allowing one to infer the pharmacophore from a series of these structure-activity relationships. The most sophisticated of these approaches use sophisticated statistical computer modeling and three-dimensional database searching to identify and design compounds or entire libraries with similar or identical pharmacophores. Identification of a pharmacophore is useful not only in drug identification and design studies, but also in lead optimization (see leads) for potency and reduction of toxicity. This is because once a pharmacophore is known, medicinal chemists can modify it to reduce toxicity while maintaining (or enhancing) potency.