From PDB to AlphaFold

Harold Varmus is a Professor of Medicine at Weill Cornell Medical College. His work has been recognized by the award of the 1989 Nobel Prize in Physiology or Medicine. He is a former Director of the NIH (1993-1999) and of NCI (2010-2015).

He sent the following comment about the change in policy at NIH in 1999 regarding the immediate release of structural data upon publication. We also asked him how this decision was influenced by his often-stated support for open science.

Like Tom Cech’s recollections, my memory of the dates and conversations pertinent to the history of making protein structural coordinates publicly accessible is a bit hazy.   But the decision to promote rapid release of such information was based heavily on the very successful adoption of a very similar policy for DNA sequence information (the Bermuda Rules), which was then being generated by the Human Genome Project.   

In addition,…

Thomas (Tom) Cech is a Distinguished Professor at the University of Colorado Boulder. He is a former President of HHMI (2000-2009). Dr. Cech's work has been recognized by the Heineken Prize of the Royal Netherlands Academy of Sciences (1988), the Albert Lasker Basic Medical Research Award (1988), the Nobel Prize in Chemistry (1989), and the National Medal of Science (1995). In 1987 he was elected to the U.S. National Academy of Sciences.

He sent the following comment about the change in policy at HHMI regarding the immediate release of structural data upon publication:

                  I appreciate your project, but my memory is hazy regarding the timeline of my own contributions (if any!) to the important requirement of depositing x-ray crystallography data on the PDB.

                  We began doing RNA crystallography in 1991, when Jennifer Doudna joined my lab as a postdoc, and began publishing structures in 1996.  I became…

Alexander Wlodawer is a Senior Investigator at the Laboratory of Cell Biology, NCI, National Institutes of Health.

He sent the following comment:

In the history you stress the role of the journals and their rules regarding deposition of both coordinates and structure factors, but I did not see one other crucial development. That was the requirement by first HHMI, and then NIH to deposit such data as a condition of being funded. I don’t remember the exact dates, but I do remember talking to Tom Cech, then the director of HHMI, convincing him that such requirements should be put in place. He also promised to talk to Harold Varmus, then director of the NIH. Very soon after that conversation the rules were officially announced. 

Philip Campbell is a former Editor in Chief of Nature. He is an astrophysicist and a Fellow of the Royal Society. He was knighted for services to science in 2015.

He sent the following comment about the change in policy at Nature and Science in 1998 regarding the immediate release of protein structural data upon publication:

Thanks for getting in touch about this topic and the valuable work on this strand of research history.

                  Background: I had the responsibility for working with colleagues in developing editorial policies for Nature and the Nature journals throughout my time as Editor in Chief of Nature (1995-2018) and then as Editor in Chief of Springer Nature, until my retirement from science publishing in 2023.

                  The substantial policy change you mention was one of the first that I can recall making. Memory plays tricks, especially over decades. However, as I recall, the trigger…