一個(gè)藥物分子經(jīng)過物理或電場(chǎng)作用形成三維功能結(jié)構(gòu)從而引起分子的藥理活動(dòng)。一般而言，藥效基因是指原子和功能基團(tuán)的結(jié)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(jīng)發(fā)展了很多研究藥物先導(dǎo)物和其針對(duì)特定靶子的可測(cè)量活性的方法，使得研究者能夠從一系列結(jié)構(gòu)活性關(guān)系中得到其藥效基因。這些方法中最成熟的是用復(fù)雜的統(tǒng)計(jì)計(jì)算機(jī)模型和三維數(shù)據(jù)庫查詢，識(shí)別和設(shè)計(jì)具有相近或相同藥效基因的復(fù)合物或整個(gè)文庫。藥效基因的識(shí)別不僅在藥物識(shí)別和設(shè)計(jì)中有用，而且對(duì)先導(dǎo)物優(yōu)化藥效減少毒性也大有用途。這是因?yàn)橐坏┲�道藥效基因，藥物化學(xué)家就可以修飾它，在保持藥效的基礎(chǔ)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.