In 1969, Berman moved to the Fox Chase Cancer Center in Philadelphia, where she worked in Jenny P. Glusker's laboratory before starting her own independent research program as a faculty member in 1973.

In June 1971, Berman attended a symposium at Cold Spring Harbor Laboratory, where several scientists agreed that data on the expanding number of protein structures should be archived in a database.

[7] At Rutgers, she continued to study nucleic acids, their interactions with proteins,[8] and also researched the structure of collagen in collaboration with Barbara Brodsky and Jordi Bella.

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.

[8][9][15][16][17] Berman was the executive producer and creator of the documentary series Target Zero which focuses on the medical as well as the social aspects of HIV treatment and prevention.

[18] The three short films interweave real-life patient stories, interviews with leading doctors, medical providers and scientists; and state of the art molecular animations.

These accounts illuminate the complex history of controlling the HIV epidemic and reveal the ongoing need for compassionate, patient-centered care and a true understanding on a cellular level the science behind the treatments.