Tools for Education

09/07

The RCSB PDB offers resources for teachers  and students; many are described in the recently-published  "Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences" (J. Appl. Cryst. (2010). 43   doi:10.1107/S002188981002371X).

 Accessible from the left hand menu, the RCSB PDB's Education section offers:

• Understanding PDB Data: Through text, images, and interactive Jmols, this feature intends to help researchers and educators get the most out of the PDB archive. Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges in exploring the archive.
• Educational Resources: This page archives many of the educational materials created by the RCSB PDB, including animations, handouts, and more.  Recent additions include an updated edition of  the Bioinformatics of Green Fluorescent Protein tutorial guide (PDF) and the How Do Drugs Work poster (PDF) and flyer (PDF).
• RCSB PDB Newsletters and Education Corner:  Published quarterly, the newsletter describes new developments, outreach efforts, and interviews with leaders in the community.  The newsletter's Education Corner, which highlights how the PDB is used in different facets of education, are also archived on a single page.  Past Education Corners have featured a rubric for biomacromolecular 3D literacy, the program Molecules for the iPhone, and physical 3D models of molecules.
• Molecule of the Month: Each Molecule of the Month installment includes an introduction to the structure and function of a particular molecule, a discussion of the relevance of the molecule to human health and welfare, suggested additional readings and resources, and interactive views.

For an introduction to the features and functionality of the RCSB PDB website, comprehensive training materials are available at openhelix.com. The training tools include

• An online narrated tutorial that demonstrates basic and advanced searching, report generation, exploring individual structures, and many other research and education tools.
• The animated PowerPoint slides from the tutorial
• Slide handouts and exercises
• Quick Reference Cards that highlight search strategies, features and functionality. The cards can be ordered at openhelix.com at no cost; shipping is free within the United States.

Short, online narrated videos describe how to use ligand searching and website customization tools.  The screencasts currently offered at the RCSB PDB site demonstrate:

• Ligand searching: Using the MarvinSketch applet
• Ligand searching: Advanced MarvinSketch features
• Ligand searching: Using SMARTS features
• Ligand searching: Loading a PDB chemical component
• Customizing Structure Summary pages using Widgets
• Tour of the left hand menu

Other educational resources are described in a downloadable flyer (PDF).

News Index

• 12/28 Happy Holidays

• 12/21 Deposition Session Restart IDs

• 12/14 Annual Report Published

• 12/07 Latest Website Release

• 12/07 Poster Prize Awarded at AsCA

• 11/30 Learn About Viruses

• 11/30 New and Improved Web Services for Accessing PDB Data

• 11/23 New Ligand Summary Pages

• 11/16 Explore Search Results Using Data Distribution Summaries

• 11/09 Creating Tabular Reports

• 11/02 PDBMobile

• 10/26 Newsletter Published

• 10/19 Binding Affinity Data Integrated with RCSB PDB

• 10/12 Categorized View of Molecule of the Month

• 10/05 Latest Website Release

• 09/28 Poster Prize Awarded at ECM

• 09/28 Analyze small molecule interactions in the PDB with Ligand Explorer

• 09/21 Redesigned BioSync

• 09/14 Exploring Search Results

• 09/07 Tools for Education

• 08/31 Newsletter Published

• 08/24 New Flyers Available

• 08/24 Poster Prize Awarded at ACA

• 08/17 Upcoming Meeting: PDB Symposium at ACS

• 08/10 wwPDB News: Validation Report PDFs

• 08/10 ADIT 2.0 Offers Improved Deposition Process

• 08/03 Poster Prize Awarded at ISMB

• 07/27 Looking at Structures: A Resource for Learning About PDB Data

• 07/27 Paper Published

• 07/20 Upcoming Meeting: ACA

• 07/20 New Release of pdb_extract Available Online and for Download

• 07/13 Get the Latest wwPDB News

• 07/06 ISMB and 3DSIG Meetings

• 07/06 Improved Version of ADIT Available

• 06/29 Use Ligand Expo When Depositing Structures with Ligands

• 06/29 Version 2 NMR Restraint Files Available from the wwPDB FTP

• 06/22 Latest Structures Widget

• 06/15 Papers published

• 06/08 New Website Features

• 06/08 Improved Version of ADIT Available, Transitional Implementation Starts June 14

• 06/01 Create a Collage of Structures

• 05/25 Search the RCSB PDB in Your Web Browser

• 05/18 Turn Your Computer into a PDB Structure Kiosk

• 05/11 New Website Features and Widgets

• 05/04 wwPDB To Provide Validation Reports as PDFs

• 05/04 Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010

• 04/27 Newsletter Published

• 04/20 Screencasts Demonstrate RCSB PDB Features

• 04/20 DNA Day: April 23

• 04/13 Exhibiting at Experimental Biology (April 24-28)

• 04/13 Come build virus models at Rutgers Day (April 24)

• 04/06 Bookmark and Share RCSB PDB Webpages

• 03/30 Advanced Search: Sequence Motif

• 03/23 San Diego Science Festival Expo Day: March 27

• 03/23 West Windsor Plainsboro High School North Wins New Jersey Science Olympiad Protein Modeling State Finals

• 03/16 Exhibiting at NSTA

• 03/09 Improved Ligand Searching

• 03/02 New Website Features

• 02/23 Online Narrated Tutorial Demonstrates How to Use the RCSB PDB

• 02/23 Changes to the wwPDB Policy for Depositing Polypeptide Structures

• 02/16 Exhibition at the Biophysical Society Meeting

• 02/09 Poster Download: How Do Drugs Work?

• 02/02 Newsletter Published

• 02/02 wwPDB FTP Advisory Notice

• 01/26 Comparison Tool for Exploring Sequence and Structure Alignments

• 01/19 NJ Science Olympiad Protein Modeling Results

• 01/12 Time-stamped Copies of PDB Archive Available via FTP

• 01/05 2009 Annual Report Published