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 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
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
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