How community has shaped the Protein Data Bank

Abstract

Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules. Since then, the number, size, and complexity of structural models have continued to grow, reflecting the productivity of structural biology. Managed by the Worldwide PDB organization, the PDB has been able to meet increasing demands for the quantity of structural information and of quality. In addition to providing unrestricted access to structural information, the PDB also works to promote data standards and to raise the profile of structural biology with broader audiences. In this perspective, we describe the history of PDB and the many ways in which the community continues to shape the archive.

Figure 1. Growth of the PDB Archive

(A) The number of entries deposited (orange) and the total number of entries available in the archive (green) each year. (B) Average molecular weight of entries in the archive from NMR (orange) and X-ray (for the asymmetric unit, green) experiments, by year of entry release. The spike seen in 1984 is the result of the release of a tomato bushy stunt virus structure (2TBV) (Hopper et al., 1984).

Figure 2. Past and Present PDB People, in Attendance at PDB40

Front row, from left to right: Francis Bernstein, Martha Quesada, Gerard J. Kleywegt, Tom Koetzle, Helen M. Berman, Haruki Nakamura, John Markley, Miri Hirshberg, and Joel Sussmann. Second row: Judith L. Flippen-Anderson, Peter Rose, Gary L. Gilliland, T.N. Bhat, Jasmine Young, Buvaneswari Coimbatore Narayanan, Monica Sekharan, Irina Persikova, and Sutapa Ghosh. Third row: Spencer Bliven, Shuchismita Dutta, Guanghua Gao, Zukang Feng, Tom Oldfield, David Micallef, Luigi Di Costanzo, Catherine L. Lawson, Sanchayita Sen, Christine Zardecki, and Chisa Kamada. Fourth row: Wolfgang F. Bluhm, Chunxiao Bi, Chenghua Shao, Dimitris Dimitropoulos, Andreas Prlić, Geoffrey Barton, Sameer Velankar, Brian Hudson, Vladimir Guranović, John Westbrook, Philip E. Bourne. Back row: Margaret Gabanyi, Eldon Ulrich, Genji Kurisu, Atsushi Nakagawa, Nomi Ron, Lihua Tan, Maria Voigt, Huanwang Yang, Rachel Kramer Green, Greg Quinn, and David S. Goodsell. Photo by Constance Brukin.

Figure 3. Frederic M. Richards Initiated This Petition to Develop Deposition Policies for PDB Data

The full petition was signed by hundreds of scientists and sent to various journals.

Figure 4. Participants in the 2011 wwPDB Format Workshop in Cambridge, UK and Comparison of File Formats

(A) Workshop participants: Top row, from left to right: Sameer Velankar, Paul Adams, Randy Read, Thomas Womack, John Westbrook, Gerard Kleywegt, and Eugene Krissinel. Middle row: John Ionides, Garib Murshudov, Helen Berman, Gérard Bricogne, and Tom Oldfield. Bottom row: Oliver Smart, Paul Emsley, and Ralf Grosse-Kunstleve. (B and C) PDB and PDBx/mmCIF file formats for representing atomic coordinate data.