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Educational Resources

Kiosk Viewer  |  Posters  |  Website Tutorials  |  Animations  |  Activities/Lessons  |  Exhibit Materials  |  Events  |  Poster Prize

These Educational Resources are aimed at teachers and students interested in learning about protein and nucleic acid structures, and how to use the RCSB PDB site (PDF Overview). For researchers and educators interested in how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges in exploring the archive, please see the Looking at Structures feature.


Molecules in Motion Kiosk Viewer

The Molecules in Motion Kiosk Viewer is a full-screen animation program that displays structures from different angles and perspectives, and focuses on chemical components within the structure.

The Kiosk program runs on Mac, Windows and some versions of Linux (i.e. CentOS 5) only, and requires the latest version of Java. The program automatically downloads coordinate files into a folder, which lets users run Kiosk on an offline computer. To customize the list of structures displayed in Kiosk, right click on the Kiosk Viewer link and save the file with a new name (with the .jnlp extension), for example myFavorites.jnlp. Edit the PDB IDs listed in the file and save it. Double click to launch Kiosk Viewer; press the Esc key to exit Kiosk Viewer.

Launch Kiosk by providing a comma separated list of PDB ids: (Java required)

By default Kiosk will display biological assemblies (if available). Uncheck here to view asymetric units only.
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Posters

Available only as a download, the poster (31Mb) "Molecular Machinery: A Tour of the Protein Data Bank" features illustrations of 75 select structures from the PDB, showing their relative sizes at a scale of three million to one, and generally describes their critical roles in the functions of living cells. A 2-sided, 8 1/2" x 11" quick reference guide (5Mb) is also available.
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Calendars

The RCSB PDB created a 2008 calendar (PDF) that uses detailed images and text to highlight DNA, transcription factors, RNA polymerase, ribosomes, chaperones, photosynthesis, actin, proteins related to transport, storage, calcium sensing, recptors, g-proteins, antibodies, and proteasomes.

The PSI Structural Genomics Knowledgebase compiled their PSI Featured Molecule series into a 2010 calendar (PDF).

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Website Tutorials

The following tutorials demonstrate how to use: Advanced Search; RCSB PDB navigation tools; the Medical Subject Headings (MeSH) Browser; and molecular viewers Protein Workshop, KiNG, and Jmol. All require the Adobe Flash player download.

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Animations

Molecular Animation Q&A

An interview with the Molecular Animators Gaël McGill, Ph.D. and Graham Johnson

Molecule of the Month Animations

Molecule of the Month images have been animated to show the large and small subunits of the ribosome, and to show oxygen binding in hemoglobin. Right-click on the animations to download.
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Activities/Lessons

Green Fluorescent Protein Tutorial

Exploring the Bioinformatics of Green Fluorescent Protein (PDF ) uses visualization tools from the RCSB PDB website to explore this protein.

Handheld 3D Virus Model

Create a 3D model of the dengue virus by printing out this PDF, cutting out protein structure, and folding. Tape or glue the flaps into place to form an icosahedron. The RNA genome, which contains 10,649 nucleotides, can be modeled using a piece of string approximately 5.4 meters long and placed inside of the structure.

Virus Structure Lecture, Lesson Plans, and Activities

A lecture (PPT) and lesson plans describing Virus Shape and Structure (PDF) and the Life Cycle of the Dengue Virus (PDF) are available for middle and high school classrooms.  These resources include templates to make 3D paper models of disease-causing viruses and review questions.

Other activies and lessons are described in past editions of the RCSB PDB's Education Corner.

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Exhibit Materials

Art of Science

The Art of Science traveling exhibit includes pictures available from the RCSB PDB website and Molecule of the Month features. If you would be interested in sponsoring this exhibit at your institution or would like more information, please let us know at info@rcsb.org.

PDB Structures on Exhibit at the Birch Aquarium

An interactive kiosk at the The Sea of Genes exhibit at the Birch Aquarium (La Jolla, CA) displayed information about specific proteins found in marine organisms – and in the PDB. The Flash animation used in the exhibit and a flyer describing it are available.

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Events

NJSO

The Protein Modeling Trial Event at the NJ Regional and State Science Olympiads is sponsored by the RCSB PDB. The website offers a variety of materials to help teams build 3D models of proteins.

Rutgers Day and the San Diego Science Festival

The RCSB PDB enthusiastically participates in activities with local communities, including the San Diego Science Festival and Rutgers Day.

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RCSB PDB Poster Prize

The RCSB PDB awards a poster prize for the best student poster presentation at a number of different meetings throughout the year.
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