一個藥物分子經過物理或電場作用形成三維功能結構從而引起分子的藥理活動。一般而言，藥效基因是指原子和功能基團的結合，使得藥物以特定方式與靶蛋白作用并顯示藥物活性。人們已經發展了很多研究藥物先導物和其針對特定靶子的可測量活性的方法，使得研究者能夠從一系列結構活性關系中得到其藥效基因。這些方法中最成熟的是用復雜的統計計算機模型和三維數據庫查詢，識別和設計具有相近或相同藥效基因的復合物或整個文庫。藥效基因的識別不僅在藥物識別和設計中有用，而且對先導物優化藥效減少毒性也大有用途。這是因為一旦知道藥效基因，藥物化學家就可以修飾它，在保持藥效的基礎上減少毒性。

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.