Dayhoffs Atlas became a template for many indispensable tools in large portions of DNA or protein-related biomedical research. In spite of this significant contribution, Dayhoff was marginalized by the community of sequencers. The contract to manage GenBank (a technology directly related to her research), awarded in the early 1980s by the NIH, went to Walter Goad at the Los Alamos National Laboratory. The reason for this attitude was unknown, with theories ranging from sexism to a clash of values with the experimental science community. Despite the success of Dayhoffs Atlas, experimental scientists and researchers considered their sequence information very valuable and were often reluctant to submit it to such a publicly available database.
During the last few years of her life, she focused on obtaining stable, adequate, long-term funding to support the maintenance and further development of her Protein Information Resource. She envisioned an online system of computer programs and databases, accessible by scientists all over the world, for identifying protein from sequence or amino acid composition data, for making predictions based on sequences, and for browsing the known information. Less than a week before she died, she submitted a proposal to the Division of Research Resources at NIH for a Protein Identification Resource. After her death, her colleagues worked to make her vision a reality, and the protein database was fully operational by the middle of 1984.
Dayhoff died of a heart attack at the age of 57 on February 5, 1983. A fund was established after her death in 1984 to endow the Margaret O. Dayhoff Award, one of the top national honors in biophysics. The award is presented to a woman who "holds very high promise or has achieved prominence while developing the early stages of a career in biophysical research within the purview and interest of the Biophysical Society." It is presented at the annual meeting of the Biophysical Society and includes an honorarium of $2,000.
She was survived by her husband, Edward S. Dayhoff of Silver Spring; two daughters, Ruth E. Dayhoff Brannigan of College Park, and Judith E. Dayhoff of Silver Spring, and her father, Kenneth W. Oakley of Silver Spring.
Her seminal contributions as the mother of the science of bioinformatics, now routinely used as part of the process for naming bacteria, were acknowledged with a bacterium being named after her in 2020, Enemella dayhoffiae.