News

Remembering Philip E. Bourne

03/11 PDB101 News

Philip E. Bourne, one of the founding members of the Research Collaboratory for Structural Bioinformatics (RCSB), passed away on March 8, 2026. He served as RCSB PDB Associate Director from 1998-2013.

Phil was part of the original team that brought the management of the PDB to the RCSB in 1998. From database development, literature integration, and visualization tools, Phil's influence is felt in every aspect of the resource used by many millions of RCSB PDB users from around the world.

In 1998, Phil joined a team of researchers who wanted to apply developing technologies in databases and data science to the Protein Data Bank archive. Together with Helen Berman and John Westbrook at Rutgers University; Gary L. Gilliland and Phoebe Fagan at the National Institute for Standards and Technology (NIST); and Peter Arzberger with Phil at San Diego Supercomputer Center/University of California San Diego (UCSD), the team entered a re-competition for the PDB.

Phil spent the early part of his career as a crystallographer and became extremely interested in the developing field of bioinformatics. He served as chair of the International Union of Crystallography (IUCr) Computing Commission and the American Crystallography Association Data and Computing Committee. He was a core member of the inaugural macromolecular crystallographic information file (mmCIF) Working Group led by Paula Fitzgerald. PDBx/mmCIF serves as the master format of the PDB to this day. The first mmCIF dictionary consisted of 1620 definitions in a fully extensible, completely computer readable format and was approved in 1997 by the IUCr. John Westbrook was responsible for developing the Dictionary Definition Language used in mmCIF, and together with Phil, developed software and tools that work with mmCIF and organized and contributed to mmCIF workshops.

Phil also brought to RCSB a love of databases. Prior to RCSB, the group at SDSC/UCSD ​​developed and maintained databases of protein structures based on the Property Object Model (POM). Phil and Michael Gribskov were involved in both sequence and structure database development. Phil also established the Protein Kinase Resource. Together with Helge Weissig, Lynn Ten Eyck, and others, Phil created a database of the PDB that was fully searchable and operational at the time of the application that led to federal funding of the RCSB PDB.

<I>The RCSB leadership team visited the National Science Foundation to discuss the new award in 1998.<BR> Back row: John Westbrook, Phil Bourne, Peter Arzberger<BR> Front row: Gary Gilliland, Helen Berman, Phoebe Fagan<BR> </I>The RCSB leadership team visited the National Science Foundation to discuss the new award in 1998.
Back row: John Westbrook, Phil Bourne, Peter Arzberger
Front row: Gary Gilliland, Helen Berman, Phoebe Fagan

Over the years, Phil provided direction for the site at UCSD, with a focus on database development, literature integration, and visualization tools. He established key RCSB collaborations at UCSD at both the Skaggs School of Pharmacy and Pharmaceutical Sciences and the San Diego Supercomputer Center. He mentored dozens of team members and students at all RCSB sites, and kept everyone on their toes in his roles as devil’s advocate and international adventurer. HIs impact on RCSB.org development is felt to this day.

<I>RCSB PDB activities over the years</I>RCSB PDB activities over the years

See Also

Selected References

  • Bourne, P. E., H. M. Berman, B. McMahon, K. D. Watenpaugh, J. D. Westbrook, and P. M. Fitzgerald. "Macromolecular Crystallographic Information File." Methods Enzymol (1997) 277: 571–90. https://dx.doi.org/10.1016/s0076-6879(97)77032-0.
  • Smith, C., M. Gribskov, I.N. Shindyalov, S.S. Taylor, L. Ten Eyck, S. Veretnik, and P.E. Bourne. "The Protein Kinase Resource." Trends Biochem. Sci. (1997) 22: 444–46.
  • Weissig, H., I.N. Shindyalov, and P.E. Bourne. "Macromolecular Structure Databases: Past Progress and Future Challenges." Acta Cryst. 54 (1998): 1085–94.
  • Bourne, P.E., M. Gribskov, G. Johnson, J. Moreland, and H. Weissig. A Prototype Molecular Interactive Collaborative Environment (MICE). Pacific Symposium on Biocomputing. Edited by R. Altman, K. Dunker, L. Hunter, and T. Klein, 1998.
  • Shindyalov, I.N., and P.E. Bourne. "Protein Structure Alignment by Incremental Combinatory Extension of the Optimum Path." Protein Eng. (1998) 11: 739–47. https://dx.doi.org/10.1093/protein/11.9.739.
  • Westbrook, J., and P.E. Bourne. "STAR/mmCIF: An Extensive Ontology for Macromolecular Structure and Beyond." Bioinformatics 16 (2000): 159–68.
  • Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. "The Protein Data Bank." Nucleic Acids Res (2000) 28: 235–42. https://dx.doi.org/https://doi.org/10.1093/nar/28.1.235.
  • Berman, H.M., J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne. "The Protein Data Bank, 1999 -." In International Tables for Crystallography. Edited by M.G. Rossmann and E. Arnold. Vol. F. Crystallography of Biological Macromolecules. Dordrecht: Kluwer Academic Publishers, 2001.
  • Bhat, T. N., P. Bourne, Z. Feng, G. Gilliland, S. Jain, V. Ravichandran, B. Schneider, K. Schneider, N. Thanki, H. Weissig, J. Westbrook, and H. M. Berman. "The PDB Data Uniformity Project." Nucleic Acids Res (2001) 29: 214–8. http://www.ncbi.nlm.nih.gov/pubmed/11125095.
  • Greer, D.S., J.D. Westbrook, and P.E. Bourne. "An Ontology Driven Architecture for Derived Representations of Macromolecular Structure." Bioinformatics (2002) 18: 1280–81.
  • Westbrook, J., Z. Feng, S. Jain, T. N. Bhat, N. Thanki, V. Ravichandran, G. L. Gilliland, W. Bluhm, H. Weissig, D. S. Greer, P. E. Bourne, and H. M. Berman. "The Protein Data Bank: Unifying the Archive." Nucleic Acids Res (2002) 30: 245–8. http://www.ncbi.nlm.nih.gov/pubmed/11752306.
  • Berman, H. M., T. Battistuz, T. N. Bhat, W. F. Bluhm, P. E. Bourne, K. Burkhardt, Z. Feng, G. L. Gilliland, L. Iype, S. Jain, P. Fagan, J. Marvin, D. Padilla, V. Ravichandran, B. Schneider, N. Thanki, H. Weissig, J. D. Westbrook, and C. Zardecki. "The Protein Data Bank." Acta Crystallogr D Biol Crystallogr (2002) 58: 899–907.
  • Berman, H. M., D. S. Goodsell, and P. E. Bourne. "Protein Structures: From Famine to Feast." American Scientist (2002) 90: 350–59. https://dx.doi.org/10.1511/2002.27.785.
  • Bourne, P. E., K. J. Addess, W. F. Bluhm, L. Chen, N. Deshpande, Z. Feng, W. Fleri, R. Green, J. C. Merino-Ott, W. Townsend-Merino, H. Weissig, J. Westbrook, and H. M. Berman. "The Distribution and Query Systems of the Rcsb Protein Data Bank." Nucleic Acids Res (2004) 32: D223–5. https://dx.doi.org/10.1093/nar/gkh096.
  • Moreland, J. L., A. Gramada, O. V. Buzko, Q. Zhang, and P. E. Bourne. "The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications." BMC Bioinformatics (2005) 6: 21.
  • Bourne, P.E. "Will a Biological Database Be Different from a Biological Journal?", PLoS Comput Biol (2005) 1: 179–81.
  • Prlic, A., S. Bliven, P. W. Rose, W. F. Bluhm, C. Bizon, A. Godzik, and P. E. Bourne. "Pre-Calculated Protein Structure Alignments at the Rcsb Pdb Website." Bioinformatics (2010) 26: 2983–5. https://dx.doi.org/10.1093/bioinformatics/btq572.
  • Prlic, A., M. A. Martinez, D. Dimitropoulos, B. Beran, B. T. Yukich, P. W. Rose, P. E. Bourne, and J. L. Fink. "Integration of Open Access Literature into the RCSB Protein Data Bank Using Biolit." BMC Bioinformatics (2010) 11: 220. https://dx.doi.org/10.1186/1471-2105-11-220.
  • Rose, P. W., B. Beran, C. Bi, W. F. Bluhm, D. Dimitropoulos, D. S. Goodsell, A. Prlic, M. Quesada, G. B. Quinn, J. D. Westbrook, J. Young, B. Yukich, C. Zardecki, H. M. Berman, and P. E. Bourne. "The RCSB Protein Data Bank: Redesigned Web Site and Web Services." Nucleic Acids Res (2011) 39: D392–401. https://dx.doi.org/10.1093/nar/gkq1021.
  • Bourne, P., and W. A. Warr. "An Interview with Phil Bourne, Associate Director of the RCSB Protein Data Bank." J Comput Aided Mol Des (2012) 26: 165–7. https://dx.doi.org/10.1007/s10822-012-9555-0.
  • Prlic, A., A. Yates, S. E. Bliven, P. W. Rose, J. Jacobsen, P. V. Troshin, M. Chapman, J. Gao, C. H. Koh, S. Foisy, R. Holland, G. Rimsa, M. L. Heuer, H. Brandstatter-Muller, P. E. Bourne, and S. Willis. "Biojava: An Open-Source Framework for Bioinformatics in 2012." Bioinformatics (2012) 28: 2693–5. https://dx.doi.org/10.1093/bioinformatics/bts494
  • Rose, P. W., C. Bi, W. F. Bluhm, C. H. Christie, D. Dimitropoulos, S. Dutta, R. K. Green, D. S. Goodsell, A. Prlic, M. Quesada, G. B. Quinn, A. G. Ramos, J. D. Westbrook, J. Young, C. Zardecki, H. M. Berman, and P. E. Bourne. "The RCSB Protein Data Bank: New Resources for Research and Education." Nucleic Acids Res (2013) 41: D475–82. https://dx.doi.org/10.1093/nar/gks1200.
  • Gao, J., A. Prlic, C. Bi, W. F. Bluhm, D. Dimitropoulos, D. Xu, P. E. Bourne, and P. W. Rose. "Biojava-Modfinder: Identification of Protein Modifications in 3D Structures from the Protein Data Bank." Bioinformatics (2017) 33: 2047–49. https://dx.doi.org/10.1093/bioinformatics/btx101
  • Wilkinson, M. D., M. Dumontier, I. J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. W. Boiten, L. B. da Silva Santos, P. E. Bourne, J. Bouwman, A. J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C. T. Evelo, R. Finkers, A. Gonzalez-Beltran, A. J. Gray, P. Groth, C. Goble, J. S. Grethe, J. Heringa, P. A. t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S. J. Lusher, M. E. Martone, A. Mons, A. L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. A. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M. A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, and B. Mons. "The Fair Guiding Principles for Scientific Data Management and Stewardship." Sci Data (2016) 3: 1–9.
  • Bliven, S. E., A. Lafita, P. W. Rose, G. Capitani, A. Prlic, and P. E. Bourne. "Analyzing the Symmetrical Arrangement of Structural Repeats in Proteins with Ce-Symm." PLoS Comput Biol (2019) 15: e1006842. https://dx.doi.org/10.1371/journal.pcbi.1006842.

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