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The PDB Talks with Frances C. Bernstein

Frances C. Bernstein (Bernstein + Sons) was a member of the PDB team at Brookhaven National Laboratory from 1974 until 1998, where she personally processed or validated most of the entries 15 through 9,000 in the PDB. During this time, she was involved with the creation of the current PDB format and testing of new processing programs for this format as they were created. She has also contributed extensively to the evolving data definitions used in databases and applications programs for macromolecular studies. Ms. Bernstein's expertise has resulted in the creation of tools such as pdb2cif and the enhancement of others including AutoDep and RasMol, and she has freely provided many helpful suggestions to the RCSB.

The PDB recently interviewed Ms. Bernstein regarding her contributions to the resource.

PDB: How did you become involved with the PDB?
Ms. Bernstein: I had two young sons and was working one day per week maintaining and modifying the crystallographic software in the Chemistry Department at Brookhaven National Laboratory. Thomas Koetzle was the sole person involved with the PDB after the untimely death of Walter Hamilton and he asked me if I could work another day per week for the PDB. As the PDB grew and my sons got older, I was able to work more hours per week and then full-time for many years.

PDB: What are some of the interesting milestones of the PDB's growth that you had participated in?
Ms. Bernstein: The original data format was based on Bob Diamond's output format and in 1976 I was involved with the design of what is now known as PDB format, as well as some of the processing and validation software. I set up the original procedures to keep track of what was done in processing and the revision history of each entry. For quite some years, we were only three people at the PDB (two of these part-time) and so we all had our hands in everything that was going on. In addition to processing data, I handled data distribution and the associated record keeping, set up the mailing list, drafted newsletters, etc. As the volume of data grew and more staff were added, we all became more specialized and my focus was on data processing and the improvement of processing and checking software. The huge increase in growth of the PDB started in the early 1990's and an excellent chart is at www.rcsb.org/pdb/holdings.html#growth.

We tried to keep things as seamless as possible for depositors and users so most changes were evolutionary as computing changed. The most dramatic changes came with widespread use of e-mail and then the Internet with web pages and entries immediately available on-line.

PDB: Generally, how did the ways in which data were deposited and validated change during your time with the PDB?
Ms. Bernstein: Originally data were deposited on magnetic tape but a few data sets came on punched cards and one or two were typed from printed coordinates (and it took years to get all the typos out of those). Correspondence was typed by a secretary, processing jobs were submitted on punched cards, and the pace was very much slower. E-mail speeded up interaction with depositors and users enormously and the biggest change came when it was possible to make data freely available to everyone on the Internet. I think it is fair to say that each data deposition had things to check and resolve and we wrote code to check all entries whenever we identified something that could be systematized in software.

PDB: What would you cite as your most rewarding contribution to the PDB?
Ms. Bernstein: I have derived tremendous satisfaction from knowing that my work, and that of all the others who have worked for the PDB over the years, is facilitating some of the enormous advances in medicine, and science in general. On a more specific level, I believe that I helped the depositor community understand that we were striving for the same goal as they were: to provide the best possible data to the user community.

Frances C. Bernstein