Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Summer 2012
Number 54


Outreach and Education

Click to view a slideshow of selected Molecule of the Month features.

Molecule of the Month reaches 150

June's article on Sliding Clamps is the 150th Molecule of the Month installment. With descriptions of structures from AAA+ proteases to zinc fingers, Molecule of the Month provides an easy introduction to macromolecular structures and the PDB archive. A slideshow highlighting other milestones is available online.

Written and illustrated since January 2000 by David S. Goodsell (The Scripps Research Institute), each entry links to high resolution illustrations, suggests topics for further exploration, and hosts customized, interactive 3D molecular views. Specific structures are highlighted each month in the article, and shown in specific PDB-101 views of individual structures.

As the keystone of the PDB-101 educational resource, the Molecule of the Month supports teachers and students at all levels in their exploration of biology at a structural level.

PDB-101 supports different ways of exploring the Molecule of the Month, including:

Molecule of the Month articles are also available from the main RCSB PDB home page, top bar searches, structure search results, and individual Structure Summary pages.

Have suggestions for future Molecule of the Month columns? Let us know at info@rcsb.org!

Click to view a slideshow of selected Molecule of the Month features. Click to view a slideshow of selected Molecule of the Month features. Click to view a slideshow of selected Molecule of the Month features. Click to view a slideshow of selected Molecule of the Month features. Click to view a slideshow of selected Molecule of the Month features. Click to view a slideshow of selected Molecule of the Month features. Click to view a slideshow of selected Molecule of the Month features.

New Poster: Virus Structures

Learn about polyhedral, helical, complex, and enveloped viruses with examples drawn at approximately 900,000x magnification with a new poster that focuses on the shapes and sizes of different virus structures.

Structures from the feline distemper virus to mimivirus are highlighted.

Virus Structures (PDF) joins other posters that illustrate The Structural Biology of HIV, Molecular Machinery, How Do Drugs Work, Ribosome, and Toll-like Receptors. Download them all from PDB-101.

PDB-101 also offers virus-related lesson plans and a template to fold a model of the dengue virus.

Virus Structures was created by the RCSB PDB and the EMDataBank.

Meetings and Events

Expo Day, Rutgers Day, and Triton Day activities.

RCSB PDB participated in a variety of community events, including the San Diego Festival of Science and Engineering's Expo Day (March 24), UCSD's Triton Day (April 7), and Rutgers Day (April 28). 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 Fifth International Biocuration Conference (April 2-4, Washington, DC) that was hosted by The Protein Information Resource (PIR). RCSB PDB's Lead Biocurator Jasmine Young co-chaired a session on Protein structure, complexes, interactions with Sona Vasudevan (PIR), and presented a poster on the Worldwide Protein Data Bank: Current Projects. Annotator Marina Zhuravleva gave a presentation on Assessment of Structure-Model Quality and Validation of Macromolecular Structures at the Protein Data Bank.

At the Experimental Biology meeting (April 21-25, San Diego, CA), the RCSB PDB met with researchers and educators at the exhibit booth. Attendees, particularly from the American Society for Biochemistry and Molecular Biology, were interested in the new searching and reporting features of the RCSB PDB website.

Director Helen Berman gave the keynote lecture for the NJ Women in Science & Technology Workforce Summit on June 15 (hosted by the NJ State Employment and Training Commission).

Upcoming meetings include:

ISMB and 3Dsig: This year, the International Society for Computational Biology is celebrating the 20th year of the ISMB-Intelligent Systems for Molecular Biology-conference (July 15-17. Long Beach, CA).

Presentations will include Internal pseudo-symmetry in proteins (Andreas Prlić) and Efficient searching and mining of the RCSB Protein Data Bank (Peter Rose).

At the ISMB Special Interest Group meeting Bioinformatics Open Source Conference (BOSC), Andreas Prlić will also present How to use BioJava to calculate one billion protein structure alignments at the RCSB PDB website.

At the 3Dsig:Structural Bioinformatics & Computational Biophysics satellite meeting, John Westbrook will discuss Format déjà vu: PDBX/MMCIF, the new data format for the wwPDB. Molecule of the Month author David Goodsell will describe Communicating and Interacting with the Molecular Cell (along with Arthur Olson). 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 Structure and Function Prediction.

ACA: At the Annual Meeting of American Crystallographic Association (July 28-August 1; Boston, MA), the RCSB PDB will be exhibiting alongside the Structural Biology Knowledgebase. Director Helen Berman will present Data Management of Small Molecule Ligands, Antibiotics, and Peptide Inhibitors in the PDB during the session on Structure-Guided Drug Discovery. Lead Annotator Jasmine Young will give an update of Current Projects of the Worldwide Protein Data Bank.

David Goodsell will be participating in Crystallography: World of Wonders, a workshop that will provide high school teachers with the materials and knowledge needed to introduce crystallography to their classrooms. The RCSB PDB Poster Prize will be awarded for the best student poster involving macromolecular crystallography.

Protein Society: Helen Berman is the 2012 Awardee of the Carl Brändén Award of the Protein Society (August 5-8; San Diego, CA). The Award, sponsored by the Rigaku Corporation, is given to an outstanding protein scientist who has also made exceptional contributions in the areas of education and/or service to the science. During the Plenary Awards Session, she will present Trendspotting from the Protein Data Bank, which will look at different trends seen in the data archive, and what they might mean for the future of biology

Congratulations to National Protein Modeling Champions

First place New Trier High School and MHC models. Images from CBM. The National Science Olympiad Tournament was held May 18-19 at the University of Central Florida. Teams built a model of MHC 1hsa, and brought along their prebuilt models of caspase protein 1i3o. The top scoring teams in this event were:

  1. New Trier High School (IL)
  2. Troy High School (CA)
  3. Camas High School (WA)
Protein modeling is managed by the MSOE Center for BioMolecular Modeling (CBM) and hosted in NJ by the RCSB PDB. This event will be on hiatus from the tournament for two years as other events are incorporated. The RCSB PDB's related Twitter account @buildmodels will continue to post education and PDB-related news and links.