Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Spring 2013
Number 57


Outreach and Education

Poster Prize Awarded at AsCA

Yohta Fukuda

The RCSB PDB Poster Prize went to Yohta Fukuda at the Joint Meeting of the Asian Crystallographic Association (AsCA), Society of Crystallographers in Australia and New Zealand (SCANZ) and the BRAGG Symposium (December 2 - 6, 2012, Adelaide, Australia) for Atomic resolution structure of copper-containing nitrite reductase provides insights into common properties of type 2 copper-containing enzymes (Yohta Fukuda,1 Taro Tamada,2 Hideto Takami,3 Tsuyoshi Inoue,1 Masaki Nojiri;1

1Osaka University, 2Japan Atomic Energy Agency, 3Japan Agency of Marine-Earth Science and Technology).

Yohta will receive Computational Structural Biology (Torsten Schwede, Manuel C. Peitsch, editors) and International Tables of Crystallography Volume F.

Many thanks to Charlie Bond (University of Western Australia) and AsCA.

ASBMB Honors RCSB PDB Director

Helen Berman is the 2013 Awardee of the DeLano Award for Computational Biosciences of the American Society for Biochemistry and Molecular Biology. The Award, established by family, friends and colleagues to honor the legacy of Warren L. DeLano, recognizes scientists for the most accessible and innovative development or application of computer technology to enhance research in the life sciences at the molecular level.

This award recognizes her accomplishments toward enabling a freely available and uniform worldwide archive of 3D structural information for biomedical research and education. Prof. Berman's passion for making structural data accessible and understandable by a broad community has driven the development of the Protein Data Bank into a vital and accessible international resource for biology. In the early 1970s, Berman was a champion of the open access of scientific information; while obvious today, at that time the concept of open access was truly visionary.

The award will be conferred at the ASBMB's Annual Meeting (April 20-24, 2013) in Boston, MA. Prof. Berman will present her award lecture, PDB as a public resource for enabling protein science, on Monday, April 22. For the full list of awardees, please see asbmb.org.

A.M. Gronenborn's Author Profile

Author Profiles: Timeline Display of a Researcher's Structures

Author Profiles are a unique historical and educational tool offering a timeline display of all structures associated with a particular researcher. Structures are sorted by deposition date, with the first instance of a protein or protein complex highlighted. Images are linked to the Structure Summary page for the entry.

A search box is provided to search by author or structural genomics center name. Author Profile URLs are permanent links that can be copied and shared.

Read Molecule of the Month articles in RCSB PDB Mobile.

Portable Molecules (of the Month)

The RCSB PDB Mobile app for Apple iOS provides fast access to PDB searching and molecular visualization.

The entire catalog of Molecule of the Month articles is available. Each feature describes important biological molecules and how they function with descriptive text and illustrations. The molecules used as examples in the articles can be further explored and viewed in 3D.

A version of the app for the Android platform will be announced shortly.

Art of Science exhibits in Giza, Egypt

SIRA CORP recently displayed the Art of Science show.

SIRA CORP hosted a Protein Science Museum using images from the RCSB PDB's Art of Science exhibit. The event was part of the Biotechnology Symposium 2013 held March 16, 2013 at Cairo University. The first of its kind in Egypt, this display and event targeted junior researchers as well as Biotechnology undergraduate students.

SIRA CORP is a consulting and training company focusing on bridging the gap between Egypt and the advanced world in critical science and technology disciplines. For more information, see www.sira-corp.com and www.facebook.com/SiraCorpBiotechnology.

wwPDB News

Special issue of Biopolymers Continues PDB40 Celebration

The March 2013 issue of Biopolymers contains six invited contributions based on presentations made at the October 2011 symposium held at Cold Spring Harbor Laboratory that commemorated 40 years of the Protein Data Bank archive.

This special issue was edited by Stephen K. Burley and Kenneth J. Breslauer, and begins with an editorial describing the history of the PDB from its beginnings through the 2011 celebration. Articles include:

  • PDB40: The Protein Data Bank celebrates its 40th birthday, Stephen K. Burley
  • Studying and polishing the PDB's macromolecules, Jane S. Richardson and David C. Richardson
  • Abstracting knowledge from the Protein Data Bank, Nicholas Furnham, Roman A. Laskowski and Janet M. Thornton
  • The impact of influenza hemagglutinin fusion peptide length and viral subtype on its structure and dynamics, Justin L. Lorieau, John M. Louis and Ad Bax
  • Sweet entanglements-protein: Glycan interactions in two HIV-inactivating lectin families, Leonardus M. I. Koharudin and Angela M. Gronenborn
  • A primer in macromolecular linguistics, David B. Searls
The issue concludes with an article by the wwPDB directors describing The Future of the Protein Data Bank.

The program and selected presentations from the October 2011 meeting are available online from the wwPDB website.

Biopolymers Special Issue:
PDB40: The Protein Data Bank Celebrates its 40th Birthday Volume 99, Issue 3, pages 165–222, March 2013 http://onlinelibrary.wiley.com/doi/10.1002/bip.v99.3/issuetoc