Analysis of protein 3D structures is a more mature field than biological sequence analysis. The Protein Data Bank started distributing coordinates of macromolecular crystal structures in the early 1970s, and since that time, many research groups and companies have developed software to visualize and measure the properties of protein structures.
Visualization of structure and measurement of structural properties are important tools for molecular and structural biologists. Being able to "see" the 3D structure of a protein and analyze its shape in detail can suggest the location of catalytic sites and interaction sites, and can help identify targets for the site-directed mutagenesis studies that are so often used to arrive at a detailed characterization of a protein's functional chemistry.
Here are some recent applications of this type of approach in molecular biology:
Molecular modeling of an allergy-causing protein from mountain cedar pollen and subsequent identification of the region that causes allergic response
Characterization of the mutagenic active site in DNA reverse transcriptase from the HIV virus; this site is thought to be responsible for the ability of the HIV virus to mutate rapidly
Modeling of a DNA binding protein involved in Bloom syndrome, and characterization of the mutations that cause the disease
There are many specialized analysis programs in the protein structure literature, and we ...