At Rutgers, she continued to study nucleic acids, their interactions with proteins, and also researched the structure of collagen in collaboration with Barbara Brodsky and Jordi Bella. She is listed as a depositor on 38 structures in the PDB from 1992 to 2011, of protein/nucleic acid complexes and their components (e.g. 1RUN, 3SSX, 2B1B), collagen fragments (e.g. 1CGD, 1EI8), and other macromolecules. In 1998, Berman and Philip Bourne together competed for and won the contract for the Protein Data Bank and the database moved from Brookhaven to the auspices of the Research Collaboratory for Structural Bioinformatics (RCSB), currently a collaboration between Rutgers and the University of California, San Diego. With colleagues, Berman redesigned the data management system, added new user tools, and made the database searchable. Since 2003, the PDB archive has been managed by the worldwide Protein Data Bank (wwPDB), a partnership founded by Berman that consists of organizations that act as deposition, data processing and distribution centers for PDB data – the RCSB, the PDBe in Europe, and the PDBj in Japan. In 2006 the BioMagResData (BMRB) databank for Nuclear Magnetic Resonance (NMR) structures became the fourth member of the wwPDB. As of July, 2018, the NDB holds over 9600 nucleic acid structures and the PDB holds more than 142,000 macromolecular structures. Also led by the RCSB, the Protein Structure Initiative (PSI) Structural Genomics Knowledgebase was launched in the Spring of 2008 to provide a continuously updated portal to research data and other resources from the PSI efforts. Berman has also been active in the scientific community, serving as president of the American Crystallographic Association in 1988, advising both the National Institutes of Health and the National Science Foundation, and serving on the editorial board of several journals. Her work has been widely published in peer reviewed scientific journals. Berman has been married twice, to engineer Victor Berman in the 1960s, and to molecular biologist Peter Young from 1976 to 1999. From the second marriage she has a son, Jason Asher Young (born 1979), a physicist. During the 1980s, Berman was diagnosed with breast cancer. The experience made her more focused in her life and her career, and interested in supporting other women who face the same diagnosis.