结构基因组学是一门用结构生物学方法研究整个生物体、整个细胞或整个基因组中所有的蛋白质和相关蛋白质复合物的三维结构的学科。主要利用实验方式（X射线晶体学、核磁共振波谱法和电子显微学）来测定蛋白质结构，同时结合同源建模（homology modelling）这一计算方式来推测蛋白质结构。和传统结构生物学不同的是，利用结构基因组学所测定的蛋白质结构通常是功能未知的蛋白质。这令科学家创立了结构生物信息学，利用三维结构信息来预测蛋白质功能。结构基因组学重视快速、高通量（high throughput）的蛋白质结构测定，而同步辐射装置是实现这一目标的重要实验装置之一。

Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large number of sequenced genomes and previously solved protein structures allows scientists to model protein structure on the structures of previously solved homologs.