Newsletter | Fall 2015 ⋅ Number 67

Outreach and Education

Download the 2014 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

This review highlights many RCSB PDB accomplishments, including support for large structures, the new Gene View illustrating correspondences between the human genome and 3D structure, and the HIV Video Challenge for high school students.

wwPDB efforts, including deposition statistics and the common Deposition & Annotation System, are also highlighted.

These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive. This edition, the RCSB PDB's fifteenth, is available as a PDF download. If you would like a printed copy, please send your postal address to

The RCSB PDB Poster Prize is awarded for the best student poster presentations at selected meetings. Recipients receive an educational book.

    Bénédicte Lafumat

    Ashley Conard

    Marina E. Ivanova

    Kunhua Li

    Dana Vuzman

  • ECM

    At the 29th European Crystallographic Meeting (Rovinj, Croatia; August 23-28), the RCSB PDB Poster Prize was awarded to Bénédicte Lafumat for Structural basis for sensitivity of fluorescent proteins to molecular oxygen investigated by high-pressure crystallography (Bénédicte Lafumat,(1) Antoine Royant,(1,2) Eve de Rosny,(2) Peter van der Linden,(1) Gordon Leonard,(1) Philippe Carpentier;
    (1) 1European Synchrotron Radiation Facility, Grenoble, France
    (2) Institut de Biologie Structurale, Grenoble, France.
    Many thanks to the judges Eleanor Dodson (University of York), Marjolein Thunissen (The MAX IV Laboratory), and Isabel Uson (Molecular Biology Institute of Barcelona), and organizer Biserka Prugovečki.


    At this summer's International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology (Dublin, Ireland; July 10-14), the RCSB PDB Poster Prize was awarded to Ashley Conard for Determining the winning SH3 coalition: how cooperative game theory reveals the importance of domain residues in peptide binding (Ashley Conard, Elisa Cilia, Tom Lenaerts, Université Libre de Bruxelles, Belgium).

    Many thanks to the judges Tatyana Goldberg (TUM), Benjamin Good (TSRI), Casey Greene (Penn Medicine), Francis Ouellette (Ontario Institute for Cancer Research), Yana Bromberg (Rutgers), Hagit Shatkay (U Delaware), Donna Slonim (Tufts), Jeroen de Ridder (Delft University), Chen Keasar (Ben Gurion University), Rob Finn (Pfam), Barry Grant (U Michigan), and organizers Iddo Friedberg (Iowa State University) and Steven Leard (ISMB).

  • ACA

    At the American Crystallographic Association's Annual Meeting (July 25-29, Philadelphia, PA), the RCSB PDB Poster Prize was awarded to Marina E. Ivanova for Molecular Interactions Within the Crumbs Cell Polarity Complex (Marina E. Ivanova, Peter Saiu, Georgina C. Fletcher, Nicola O'Reilly, Andrew G. Purkiss, Svend Kjaer, Barry J. Thompson, Neil Q. McDonald; London Research Institute Cancer Research UK).

    Kunhua Li received an honorable mention for High Resolution Crystal Structures of Antiviral, Glycosylated Y3 Protein from the Fungus Coprinus Comatus (Kunhua Li, Steven D. Bruner, Yousong Ding, Peilan Zhang, Guang Yang; University of Florida)

    Many thanks to the judges (Barry Finzel, Ray Salemme, Blaine Mooers) and to Marcia Colquhoun and the ACA.

  • ICSG

    At the International Conference on Structural Genomics (June 7-11, Rehovot, Israel), the RCSB PDB Poster Prize was awarded to Dana Vuzman for Gene Discovery in Undiagnosed Disease (Brigham & Women's Hospital & Harvard Med School).

    Many thanks to judges Peter Stern (Science), Luhua Lai (Chinese Academy of Sciences), Olivier Lichtarge (Baylor College of Medicine), John Norvell (Founding Director of the NIGMS Protein Structure Initiative), Scot Wherland (Washington State University) and organizers Joel Sussman (Weizmann Institute of Science) and Tom Terwilliger (Los Alamos National Laboratory).

An interactive viewer animates RCSB PDB's popular Molecular Machinery poster in 3D.

In 2014, Molecular Machinery: A Tour of the Protein Data Bank was published to celebrate the milestone 100,000 entries released in the PDB archive. Ninety-six structures illustrate the vast range of molecular shapes and sizes in the PDB. These structures are depicted relative to the cellular membrane and organized in categories related to function. A scale bar provides a sense of molecular size in nanometers.

The interactive view of Molecular Machinery lets users select a structure, access the entry in 3D using Protein Viewer (PV; requires WebGL enabled), read a brief summary of the molecule's biological role, and access the corresponding PDB entry and Molecule of the Month column.

Users can highlight structures in the Molecular Machinery viewer based on functional category. For instance, selecting "Blood Plasma" from the right menu highlights the structures shown that are involved with transporting nutrients and defending against injury.

The "Auto Mode" option will automatically launch a tour of the structures, highlighting the different categories of structures and the individual examples. The 3D view uses PV to rotate the molecule, use different depiction styles, and zoom in/out of the molecule. This mode can be used as a screensaver or as a kiosk display.

Users can access the Molecular Machinery Viewer from and from the Educational Resources > Animations section of PDB-101. This viewer was designed and developed by Robert Lowe, Maria Voigt, and David S. Goodsell.

PDB-101 resources promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public.  A video tour highlights some of the different features available.
Recently added features include the interactive Molecular Machinery viewer and the GFP paper model.
Other PDB-101 resources include:

  • Educational Resources include posters, animations, paper models, and classroom lessons and activities.
  • Molecule of the Month articles describe the structure and function of a molecule, offer interactive views and discussion topics, and links to specialized pages to help explore specific example structures.
  • The Structural View of Biology Browser feature promotes a top-down exploration of the PDB. Readers can travel through high-level functional categories (such as Protein Synthesis and Health and Disease) and descriptive subcategories (like Replication or Immune System) to access relevant articles that describe molecules in simple terms and provide specific examples.
  • Understanding PDB Data is a reference to help explore and interpret individual PDB entries. Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges to exploring the archive.
  • Video Challenge. RCSB PDB challenged high school students to tell a molecular story about HIV/AIDS, with great results.

To visit PDB-101 from the main RCSB PDB site, click on the blackboard PDB-101 logo. This view offers easy navigation: select any Molecule of the Month article from the top bar pulldown menu or choose one of the tabs to jump to other sections. Select the blue RCSB PDB logo from the top of the page at any time to return to the main website.