Heme proteins are a class of biologically important macromolecules that have a unique, common active site, an ironαprotoporphyrin IX complex. Despite the common active site, heme proteins have three distinct biological functions: reversible oxygen transport, reversible electron transfer, and metabolizing enzymes. Each type of heme protein differs in the specific forms of the heme complexes that are involved in its biological function. Not only the biological activity, but also the spectroscopic properties of the intact heme proteins are largely centered on the heme unit. Thus, for this family of proteins, there is a particularly strong link between structure spectra and function. However, experimental spectroscopic methods cannot, by themselves, yield a detailed molecular description of the heme active site in the many stable and transient forms that it assumes as a part of its function. Missing is a direct correspondence between observable properties and explicit models for these diverse stable and transient forms of the heme active site that can best be provided by computational studies. In the work reported here, the seminal role played by one of these methods, the semiempirical all-valence electron INDOrSCFrCI method, developed in the laboratory of Dr. Michael Zerner, in elucidating the structure, spectra, and function of heme proteins is demonstrated by four examples from work done in our laboratory. The goal of the first study was to elucidate the nature of the important oxyferrous species of the globins and to use it to provide a consistent explanation of the origin of the observed spectroscopic properties. The goal of the second study was to identify the origin of the signature spectrum of the ubiquitous metabolizing heme proteins, the cytochrome P450s, an intense peak at 450 nm giving them their name. The other two studies illustrate the usefulness of this method in identifying transient species in two related families of metabolizing heme proteins. These are the postulated peroxide complex of peroxidases and the putative catalytically active Compound I form of the cytochrome P450s.