Outreach and Education

PDB-101 packages together resources that promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public.

Recently added features to PDB-101's Educational Resources section include:

• Paper models. New PDFs can be used to create 3D models of the HIV capsid and Green Fluorescent Protein. Other PDFs can be used to build DNA, tRNA, and the dengue virus.
  
  
  
  
• Animation. The new video What is a Protein? illustrates the path from primary to quaternary structure. It is also available as a PDF flyer for download.
  
  

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Recent meeting participation has included:

• ISMB/ECCB

  The International Society for Computational Biology and the European Conference on Computational Biology met July 19-23 in Berlin, Germany. RCSB PDB presentations included What Bioinformaticians need to know about digital publishing beyond the PDF (Associate Director Phil Bourne) and New tools and visualization features at the RCSB PDB (Peter Rose).

  At the ISMB Special Interest Group meeting Bioinformatics Open Source Conference (BOSC), Andreas Prlić presented Ten simple rules for the open development of scientific software. At the 3Dsig:Structural Bioinformatics & Computational Biophysics satellite meeting, Associate Director Stephen Burley presented a keynote presentation and poster on wwPDB: Ensuring a freely accessible, singular archive of high quality macromolecular structure information, and Peter Rose presented A survey of protein stoichiometry and symmetry in the PDB as a talk and a poster. The 3DSig poster Aligning subunits of internally symmetric proteins with CE-Symm by Spencer Bliven was also presented.

  Associate Director Phil Bourne was one of the 3Dsig Program Chairs.

• ACA

  From July 20-24, the RCSB PDB participated in the 2013 Meeting of the American Crystallographic Association (ACA) in Honolulu, Hawaii. Attendees visited the exhibition booth to meet with members of the RCSB PDB and the PSI Structural Biology Knowledgebase, and viewed demonstrations of the new wwPDB Deposition & Annotation System. John Westbrook presented The New wwPDB Deposition and Annotation System in the session Structure Validation With The Pros and Director Helen Berman presented The wwPDB: Ensuring a single, uniform archive of high quality data in the session Enabling Partnerships for Broader Crystallographic Data Accessibility.

• ICSG2013-SLS

  At the Structural Life Science/Seventh International Conference on Structural Genomics (July 29-August 1; Sapporo, Japan), Stephen Burley (Associate Director) presented wwPDB: Ensuring a freely accessible, singular archive of high quality macromolecular structure information.

  PDBj Director Haruki Nakamura and Stephen Burley also presented a poster on The New wwPDB Deposition and Annotation System.

• ECM

  John Westbrook described the PDBx format in the presentation Crystallographic Information and Data Management as part of the COMCIFS (the IUCr Committee for the Maintenance of the CIF Standard) satellite meeting of the European Crystallographic Meeting at University of Warwick (25-29 August 2013). At the same meeting, wwPDB collaborator Sameer Velankar (PDBe) described the Deposition and validation of macromolecular structures. Abstracts and presentations have been published.

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

Peter Lee

• ACA: Peter Lee

  At ACA, the award went to Peter Lee for Head Hunting: Targeting the Influenza Hemagglutinin Receptor Binding Site (Peter S. Lee,¹ Ayato Takada,² James E. Crowe Jr.,³ Yoshikazu Kurosawa,⁴ Ian A. Wilson¹

  ¹The Scripps Research Institute, ²Hokkaido University, ³Vanderbilt University, ⁴Fujita Health University).

  Many thanks to judges Champion Deivanayagam (University of Alabama at Birmingham), Robert McKenna (University of Florida), and Clyde Smith (Stanford University); and to Marcia Colquhoun and the ACA.

• ISMB/ECCB: Matthias Dietzen

  
  Matthias Dietzen
  
  

  At ISMB/ECCB, the award went to Matthias Dietzen for Three-Dimensional Modeling of Macromolecular Assemblies by Efficient Combination of Pairwise Dockings (Matthias Dietzen,¹ Olga Kalinina,¹ Katerina Taškova,² Benny Kneissl,³ Elmar Jaenicke,³ Heinz Decker,³ Thomas Lengauer,¹ Andreas Hildebrandt³

  ¹Max Planck Institute for Informatics, Saarbrücken, Germany, ²Intel Visual Computing Institute, Saarbrücken, Germany, ³Johannes Gutenberg University, Mainz, Germany)

  Many thanks to the Steven Leard, the International Society for Computational Biology, and the judges: Yana Bromberg (Chair, Rutgers), Manuel Corpas (Independent), Jeroen de Ridder (Delft University of Technology), Nils Gehlenborg (Harvard), Tatyana Goldberg (TU Munich), Edda Kloppmann (TU Munich), Geoff Macintyre (University of Melbourne), Magali Michaut (Netherlands Cancer Institute), Nikolay Samusik (Stanford), Venkata P. Satagopam (EMBL), Oren Tzfadia (Weizmann Institute of Science).


Youngchang Kim

• ICSG: Youngchang Kim

  At ICSG, the award went to Youngchang Kim for Structural Analysis of the Catalytic Mechanism of NDM-1 (Youngchang Kim,¹ Mark Cunningham,² Christine Tesar,¹ Robert Jedrzejczak,¹ Joseph Mire,² Andrew Binkowski,¹ Gyorgy Babnigg,¹ James Sacchettini,³ Andrzej Joachimiak¹

  ¹Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL, ²Physics and Geology, The University of Texas-Pan American, Edinburg, TX, ³Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX).

  Many thanks to judges Stephen Burley (RCSB PDB), Katsumi Maenaka (Hokkaido University), and Tom Terwilliger (Los Alamos National Laboratory).


Jonathan C.
Brooks-Bartlett

• ECM: Jonathan C. Brooks-Bartlett

  At ECM, the award went to Jonathan C. Brooks-Bartlett for Exploring the Relationships Between Diffracted Intensity Decay and a New Dose Metric for MX (Jonathan C. Brooks-Bartlett, Oliver B. Zeldin, Elspeth F. Garman; Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford).

  Many thanks to judges and organizers: Alessia Bacchi (University of Parma), Ralf Ficner (University of Göttingen), Dean Keeble (University of Warwick), Pietro Roversi (University of Oxford), and Marjolein Thunnissen (Lund University).

  All poster prize awardees are listed on the RCSB PDB website.