Outreach and Education
Meetings and Events
The RCSB PDB built virus models at Rutgers Day, an event of discovery and lively activities that showcase the varied resources, departments, and people at the university. More photos are posted on Facebook.
RCSB PDB participated in a variety of community events, including the San Diego Festival of Science and Engineering's Expo Day (March 23) and Rutgers Day (April 27). Activities ranged from building DNA and viruses out of marshmallows to exploration of the RCSB PDB resource.
Curators and developers of biological databases convened at the Sixth International Biocuration Conference (April 7-10; Cambridge, UK). RCSB PDB's Lead Biocurator Jasmine Young presented a poster on Curation at the PDB.
At the Experimental Biology meeting (April 20-24; Boston, MA), RCSB PDB Director Helen M. Berman received the 2013 DeLano Award for Computational Biosciences from 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 2013 award honors Prof. Berman's efforts to make data universally available.
The RCSB PDB also participated in the National Science Teacher Association's Annual Meeting, as described in this issue's Education Corner.
Upcoming meetings include:
- ISMB/ECCB and 3Dsig: The International Society for Computational Biology and the European Conference on Computational Biology will meet July 19-23 in Berlin, Germany. Presentations will include 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).
- ACA: At the Annual Meeting of American Crystallographic Association (July 20-24; Honolulu, HI), the RCSB PDB will be exhibiting alongside the Structural Biology Knowledgebase. Director Helen Berman will present The wwPDB: Ensuring a single, uniform archive of high quality data during the session on Enabling Partnerships for Broader Crystallographic Data Accessibility. John Westbrook will present a poster and a tutorial in the Structure Validation session on The New wwPDB Deposition and Annotation System.
The RCSB PDB Poster Prize will be awarded for the best student poster presentation involving macromolecular crystallography. -
ICSG2013-SLS: At Structural Life Science/Seventh International
Conference on Structural Genomics (July 29-August 1; Sapporo, Japan), Stephen Burley will present wwPDB: Ensuring a freely accessible, singular archive of high quality macromolecular structure information.
The RCSB PDB Poster Prize will be awarded for most creative use of the PDB. - ECM28: At the 28th Meeting of the European Crystallographic Association (August 25-28, Warwick, UK), John Westbrook will speak on mmCIF and Structural Bioinformatics as part of the August 25 satellite symposium on Crystallographic Information and Data Management organized by COMCIFS, the IUCr Committee for the Maintenance of the CIF Standard.
The RCSB PDB Poster Prize will be awarded for the best student poster presentation involving macromolecular crystallography.
At the ISMB Special Interest Group meeting Bioinformatics Open Source Conference (BOSC), Andreas Prlić will present Ten simple rules for the open development of scientific software.
At the 3Dsig:Structural Bioinformatics & Computational Biophysics satellite meeting, Associate Director Stephen Burley will give a keynote presentation on wwPDB: Ensuring a freely accessible, singular archive of high quality macromolecular structure information, and Peter Rose will present 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 will also be presented. Associate Director Phil Bourne is one of the 3Dsig Program Chairs.
The RCSB PDB Poster Prize will be awarded for the best student poster presentation in the category of Protein Structure and Function Prediction and Analysis.
wwPDB Symposium
A special public symposium sponsored by the wwPDB will be held on September 26, 2013 at Rutgers, The State University of New Jersey. A Celebration of Open Access in Structural Biology: Recognizing the career and achievements of Professor Helen M. Berman will include presentations from:- Jean Baum (Rutgers, The State University of New Jersey)
- David L. Beveridge (Wesleyan University)
- Wayne Hendrickson (Columbia University)
- Stephen Neidle (University College London)
- Janet Thornton (European Bioinformatics Institute | EMBL Outstation - Hinxton)
- Soichi Wakatsuki (SLAC National Accelerator Laboratory | Stanford University)
- Cynthia Wolberger (Howard Hughes Medical Institute | Johns Hopkins University School of Medicine)
New Paper: Trendspotting in the PDB
A new paper from the RCSB PDB has been published that analyzes PDB data to identify developments and trends in structural biology:
- Trendspotting in the Protein Data Bank
Helen M. Berman, Buvaneswari Coimbatore Narayanan, Luigi Di Costanzo, Shuchismita Dutta, Sutapa Ghosh, Brian P. Hudson, Catherine L. Lawson, Ezra Peisach, Andreas Prlić, Peter W. Rose, Chenghua Shao, Huanwang Yang, Jasmine Young, Christine Zardecki
FEBS Letters (2013) 587: 1036-1045
doi: 10.1016/j.febslet.2012.12.029
Create High Resolution Images
Download high resolution images from Molecule of the Month articles.
Shown: Transfer-Messenger RNA doi: 10.2210/rcsb_pdb/
mom_2013_1
Several interactive, Java-based tools7 can be used to visualize PDB data and create pictures.
Protein Workshop offers easily customized views; Simple Viewer utilizes a quick ribbon display; and Ligand Explorer visualizes the interactions of bound ligands in protein and nucleic acids structures.
Each program can be used to create and save high-resolution images in JPEG, PNG, and TIFF formats. Using the Save Image dialog box from the File menu, users can specify the width and height of an image in pixels, inches, or millimeters.
From the educational PDB-101 site, high resolution TIFFs of Molecule of the Month illustrations can be downloaded and used in presentations and publications. The high resolution files are linked from each article, and available as an archive.
PDB-101 posters, including The Structural Biology of HIV and Molecular Machinery: A Tour of the Protein Data Bank, can be saved as high or low resolution PDFs.
Citation and usage information is available at rcsb.org.
References
7. J.L. Moreland, A. Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne (2005) The Molecular Biology Toolkit (MBT): A modular platform for developing molecular visualization applications BMC Bioinformatics 6:21.