Year 2015 News Articles

Poster Prize Awarded at ACA

01-Sep-2015

At the American Crystallographic Association's Annual Meeting (July 25-29, Philadelphia, PA), the RCSB PDB Poster Prize was awarded to Marina E. Ivanova for Molecular Interactions Within the Crumbs Cell Polarity Complex (Marina E. Ivanova, Peter Saiu, Georgina C. Fletcher, Nicola O'Reilly, Andrew G. Purkiss, Svend Kjaer, Barry J. Thompson, Neil Q. McDonald; London Research Institute Cancer Research UK).

Kunhua Li received an honorable mention for High Resolution Crystal Structures of Antiviral, Glycosylated Y3 Protein from the Fungus Coprinus Comatus (Kunhua Li, Steven D. Bruner, Yousong Ding, Peilan Zhang, Guang Yang; University of Florida)

Many thanks to the judges (Barry Finzel, Ray Salemme, Blaine Mooers) and to Marcia Colquhoun and the ACA.

All 2015 awardees will be listed on the RCSB PDB website and will receive an educational book.

The RCSB PDB also participated in several other events at the ACA meeting; pictures are online.

Marina Ivanova

Marina Ivanova

Kunhua Li

Kunhua Li



Annual Report Published

25-Aug-2015

Download the 2014 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

This review highlights many RCSB PDB accomplishments, including support for large structures, the new Gene View illustrating correspondences between the human genome and 3D structure, and the HIV Video Challenge for high school students.

wwPDB efforts, including deposition statistics and the common Deposition & Annotation System, are also highlighted.

These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive. This edition, the RCSB PDB's fifteenth, is available as a PDF download. If you would like a printed copy, please send your postal address to info@rcsb.org.

2014 Annual Report

When the PDB archive was established in 1971, it contained seven structures. In 2014, the PDB passed the milestone of making more than 100,000 structures publicly available for scientific research and education. To commemorate this special milestone, RCSB PDB released an updated version of the iconic poster Molecular Machinery: A Tour of the Protein Data Bank as well as a related interactive display. This cover highlights a portion of that poster.


Take an Interactive Tour of the Protein Data Bank

18-Aug-2015

A new interactive viewer animates RCSB PDB's popular Molecular Machinery poster in 3D.

In 2014, Molecular Machinery: A Tour of the Protein Data Bank was published to celebrate the milestone 100,000 entries released in the PDB archive. Ninety-six structures illustrate the vast range of molecular shapes and sizes in the PDB. These structures are depicted relative to the cellular membrane and organized in categories related to function. A scale bar provides a sense of molecular size in nanometers.

The interactive view of Molecular Machinery lets users select a structure, access the entry in 3D using Protein Viewer (PV; requires WebGL enabled), read a brief summary of the molecule's biological role, and access the corresponding PDB entry and Molecule of the Month column.

Users can highlight structures in the Molecular Machinery viewer based on functional category. For instance, selecting "Blood Plasma" from the right menu highlights the structures shown that are involved with transporting nutrients and defending against injury.

The "Auto Mode" option will automatically launch a tour of the structures, highlighting the different categories of structures and the individual examples. The 3D view uses PV to rotate the molecule, use different depiction styles, and zoom in/out of the molecule. This mode can be used as a screensaver or as a kiosk display.

Users can access the Molecular Machinery Viewer from mm.rcsb.org and from the Educational Resources > Animations section of PDB-101. This viewer was designed and developed by Robert Lowe, Maria Voigt, and David S. Goodsell.

Interactive Tour of the PDB


Save References to Mendeley and Endnote

11-Aug-2015

Most PDB entries are associated with a primary reference. The option to download citation information for Mendeley and EndNote reference management programs has been added to Structure Summary pages. This citation information is obtained from PubMed, when available.

Download Citation Dropdown



Explore PDB Structures by Browsing Annotations

04-Aug-2015

RCSB PDB's Browse Database feature offers access to structures in the PDB archive using different hierarchical trees.

Browsers are available to find structures organized around the following classifications:


Click Browse from the top of every RCSB PDB page and then the desired Browser Tab to start searching.

Transporter Classification BrowserUse the Transporter Classification Browser to find PDB's membrane transport proteins as organized by TC Database family (www.tcdb.org). The browser will autocomplete search terms with the matching classifications, and highlight locations on the tree.



Web Services for Accessing PDB Data

28-Jul-2015

Web Services can help software developers build tools that efficiently interact with PDB data. Instead of storing coordinate files and related data locally, Web Services let software tools to access the RCSB PDB remotely. Detailed documentation for accessing these Web Services is available.

RESTful services exchange XML files in response to URL requests. RESTful search services return a list of IDs for Advanced Search and SMILES-based queries. RESTful fetch services return data when given IDs, including PDB entity descriptions, ligand information, third-party annotations for protein chains, and PDB to UniProtKB mappings.

Improvements are being made based on community feedback. Please let us know if there are website options that you think should be offered as a web service.



Summer Newsletter Published

21-Jul-2015

The Summer 2015 issue of the RCSB PDB Newsletter

The Summer 2015 issue of the RCSB PDB Newsletter is now available.

Articles describe the RCSB PDB's leadership transition anniversary, new website features for query and visualization, and the protein modeling results at the National Science Olympiad. RCSB PDB remembers Edgar Meyer and John Wooley. The Education Corner highlights the results of our High School Video Challenge.   

This issue's Education Corner highlights the results of our High School Video Challenge.

RCSB PDB's Newsletter is published and archived onlineSign up to receive electronic updates each quarter.



Membrane Query and Annotation

14-Jul-2015

Membrane proteins in the PDB have been identified and annotated to provide improved query and reporting options.

Users can quickly find all annotated membrane proteins in the PDB by entering "membrane protein" in the top bar simple search and selecting the "Retrieve Membrane Proteins" option. 

The Membrane Protein Browser and the Membrane Proteins drill-down tool from the home page and search results can be used to investigate specific membrane protein classifications and access the corresponding structures.

Membrane protein annotations for each entry appear in the Search Results and individual Structure Summary pages (example: 2rh1).

Transmembrane proteins in the PDB are identified using the mpstruc database (Stephen White, UC Irvine), sequence clustering, and data derived from UniProt. Details are available


Explore Membrane Protein Classifications using the drill-down tool from the home page (shown) or search results.


Potassium channel (PDB ID 3lut) as shown in our Molecular Machinery interactive viewer.


wwPDB Deposition Tool Replaces ADIT for Crystal Structures

07-Jul-2015

As announced in January, ADIT will be retired on July 19, 2015 for structures determined using X-ray crystallography. Any in-progress ADIT X-ray deposition sessions need to be completed before that time.

wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of a new Deposition and Annotation System. Using this system, more than 7,600 structures have been deposited and annotated, and more than 3,500 structures released in the archive.

Features of the new system include use of the PDBx/mmCIF data format, which produces more uniform data; the ability to replace data files pre- and post-deposition; enhanced communication; improved annotation; and geometric and experimental data checking based on recommendations from expert task forces. Detailed information and video tutorials are available.

ADIT will continue to accept depositions from other experimental methods. Deposition tools for NMR and 3DEM are being developed by the wwPDB.

Questions and comments should be sent to info@wwpdb.org.



Poster Prize Awarded at ICSG

07-Jul-2015

At the International Conference on Structural Genomics (June 7-11, Rehovot, Israel), the RCSB PDB Poster Prize was awarded to Dana Vuzman for Gene Discovery in Undiagnosed Disease (Brigham & Women's Hospital & Harvard Med School).

Many thanks to judges Peter Stern (Science), Luhua Lai (Chinese Academy of Sciences), Olivier Lichtarge (Baylor College of Medicine), John Norvell (Founding Director of the NIGMS Protein Structure Initiative), Scot Wherland (Washington State University) and organizers Joel Sussman (Weizmann Institute of Science) and Tom Terwilliger (Los Alamos National Laboratory).

All 2015 awardees will be listed on the RCSB PDB website and will receive an educational book.




Contact Customer Services with Questions and Feedback

30-Jun-2015

Feedback Button Click on the Feedback button at the bottom of any page to submit questions and feedback. The form accepts attachments of files and screenshots. Requests are automatically entered into a tracking system.

RCSB PDB's Customer Services collects and answers questions about the website, PDB data, and structural biology. Nearly 1000 unique users initiate electronic conversations with the RCSB PDB each year. Questions and comments come from students new to structural biology, users involved in the general study of science, and domain experts from the various disciplines that utilize PDB data.

The recent re-design of the RCSB PDB website added a "Feedback" button at the bottom of each page to make it even easier to contact Customer Services. This feedback is critical, as these comments often lead to new website features and enhancements.

Let us know what you think--we would love to hear from you.

Frequently asked questions include:

Q: How can I create a report of specific characteristics across my search results?
A: This is easy to do using the "Reports" pull-down menu from the results page. You can generate a quick report (primary citations, crystallization conditions, etc.) or a custom report of the fields that are of interest to you. All reports can be downloaded as Excel spreadsheets.

Q:I am wondering what several of the columns in the coordinate section of the PDB format files and several other sections of the file mean.  How do I find the same information in PDBx/mmCIF format?
A: Visit the PDB format guide and the PDBx/mmCIF Dictionary Resources Page, and we can help with additional questions.

Q: I want to know more about feature X, but I don't know how.  Help!
A: Sure! Many website features and enhancements have been developed in response to user requests. Recent examples include the recent implementation of the Gene View and Membrane Protein Annotation, and the ability to download citations to reference management programs.



Map Genomic Position to Protein Sequence and Structure

23-Jun-2015

A new tool can be used to map genomic position to UniProt sequence and PDB structure

For example, this tool can be used to locate the position of a SNP related to breast canceron the corresponding genomic position, UniProt sequence, and 3D structure.



The mapping tool displays the position of a SNP on the gene, the UniProt sequence, and 3D structure. By clicking on the green buttons, the consequences of this SNP at the gene, protein, and structure level can be explored.


HIV Video Challenge Awards

16-Jun-2015

For the second year in a row, the RCSB PDB invited high school students to create short videos that tell a story about HIV/AIDS. Students were tasked to include a visualization/animation of two or more molecular structures from the PDB, and include a message about the importance of testing.

2015 Video Challenge Awards

Judge's Award

Our panel of expert judges scored the videos based on scientific content (40%), creativity (20%), overall impact (10%), originality of concept (10%), entertainment value (10%), and production quality (10%).

  • First Place: Battling HIV: The Search for a Cure
    By Calvin Qian, Matthew Brown, Charles Morse, and Justin Halim of Academy of Allied Health and Science, Neptune City, NJ (Team Advisor: Richard Tempsick)



  • Second Place: The Search for a Vaccine for HIV
    By Alexa Skolnik and Maryann Zielinski of East Brunswick High School, East Brunswick, NJ (Team Advisor: Anne Sanelli)



  • Third Place: HAART: A Stop Motion Story
    By Justin May, Katarina Wang, Akshay Malavade, and Joy Song of East Brunswick High School, East Brunswick, NJ (Team Advisor: Louise Jasko)



  • Viewer's Choice Award: The Search for a Vaccine (as selected by popular vote)
    By Naszir Johnson, Henry Lucas, Matt Weiler, and Valeria Rodriguez of Engineering and Science University Magnet School, Hamden, CT (Team Advisor: Leon Tynes)


All submitted videos can be viewed online.



Science Olympiad National Protein Modeling Results

09-Jun-2015

Science Olympiad 2015

A team from Harriton High School in Rosemont, Penn. took first place in the National Science Olympiad Protein Modeling Event at the University of Nebraska-Lincoln May 15 and 16. The victory earns team members Jamie Song, Dayita Sharma, and Sarah Root a $10,000 scholarship every year for four years to attend the Milwaukee School of Engineering (MSOE), if they choose to apply to the university and are accepted.

Science Olympiad features nearly two dozen team events held at tournaments across the country. Teams are recognized for their performance in individual events and in the overall tournament. In Protein Modeling, students must prove they understand basic features of protein structure, use online visualization tools to explore and manipulate protein structures, and create 3D physical models of proteins using foam-covered wire.

The focus of this challenge was to model a fragment of the CRISPR Cas9 protein used to edit the human genome. Cas9 is a bacterial DNA nuclease enzyme that naturally functions in bacteria to protect them from invading viruses. Many researchers have recently modified the CRISPR/Cas9 system to be useful in gene-editing.

This year's protein modeling event was designed by MSOE and RCSB PDB, and highlights related Molecule of the Month columns as a resource.  Related materials about this event are hosted by MSOE and RCSB PDB.



Vote Now!

02-Jun-2015

The RCSB PDB challenged high school students to create short videos that tell a story about HIV/AIDS.

Voting for the Viewers Choice Award will be open from June 2nd 9:00am EST until June 9th 12:59 EST at education.rcsb.org/videochallenge15. Award winners will be announced at rcsb.org on June 16, 2015.

View the videos online, and then cast your vote for the Viewer's Choice Award.



Visualize in 3D with PV

26-May-2015

4FOH PV view of RuBisCO PV view of rubisco (PDB ID 4F0H).

An experimental version of the Protein Viewer (PV) has been added to the visualization options offered by the RCSB PDB for proteins and nucleic acid structures on each Structure Summary page. PV uses WebGL and enables hardware-accelerated graphics in modern web and mobile browsers.

PV can display symmetric structures aligned along the symmetry axes. It can also be launched in full screen or standalone windows.

For more information on PV, please visit http://biasmv.github.io/pv/.



Download Batches of Data

19-May-2015

The new Download Tool can be used to download multiple structure, experimental data (structure factors, NMR restraints), sequence, and ligand files in various file formats in uncompressed and compressed (gzipped) form.

Large structures without PDB-formatted files can be downloaded in PDBx/mmCIF format.  Selecting the PDB file format option for large structures will return compressed archive files (tar.gz) containing collections of minimal/best effort files in PDB format.

The Download Tool can also be used to download FASTA sequence files and SDF ligand files, with an option to download these data for the entire archive.

This tool replaces our earlier Download Applet and requires an up-to-date Java installation (Take the Browser Compatibility Test). The Download Tool is launched as a stand-alone application from the RCSB PDB website using the Java Web Start protocol.



Molecule of the Month Paper Published

12-May-2015

Read about the design of the Molecule of the Month series, and how it is used in research and education:

The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology
(2015) DS Goodsell, S Dutta, C Zardecki, M Voigt, HM Berman, SK Burley
PLoS Biol 13(5): e1002140. doi:10.1371/journal.pbio.1002140

A full list of RCSB PDB publications is available.

We are celebrating the 15th year of Molecule of the Month with a PDF calendar for 2015 that features many molecular highlights from the archive.

15 Years of Molecule of the Month
To celebrate the 15th anniversary of the Molecule of the Month, we have assembled a PDF calendar for 2015 that features many molecular highlights from the archive.


Experience the Art of Science

05-May-2015

The Art of Science exhibition highlights the fascinating 3D shapes and symmetries of biological macromolecules found in the PDB.

The show was recently seen by thousands of students while on display at McPherson College (Kansas) and The Delbarton School (NJ) through support provided by the American Crystallographic Association.

The show will be on display at the Rutgers Art Library from May 1-29. As the exhibit takes place during the University's study period and exams, "toober" materials will be on hand for students to take a study break by building models of the images shown.

The opening reception is open to the public, and will take place on Wednesday, May 6, 2015 from 4:00-5:00 pm. The Rutgers Art Library is located in Voorhees Hall at 71 Hamilton Street in New Brunswick, NJ.

Please contact info@rcsb.org if you would like to learn more about the Art of Science program.



HS Video Challenge Deadline: May 31

05-May-2015

The RCSB PDB invites high school students to create short videos (two minutes or less) that tell a story about HIV/AIDS in a new competition. The video must include a visualization/animation of two or more molecular structures from the PDB and may be focused on any topic related to the structural biology of HIV/AIDS.  Videos will be considered for three awards: Judge's Choice, Viewer's Choice, and Service to the Community. The 2014 winning videos are online for inspiration.

Many resources are offered to help students get started, including the new video Learn about HIV from the RCSB PDB. Visit PDB-101 for an overview, rules, HIV-related education materials, tutorials on making videos, and more.

The deadline for submission is May 31, 2014.




2014 Second Place: HIV: A Cellular Hijacker
By Oneida Shushe of Colonie Central High School (Team Advisor: Jason Goldberg)


Access New Website Features

28-Apr-2015

New and enhanced features have been added to the RCSB PDB resource:

  • Download data in batches. The Download Tool can download groups of structures, experimental data files, sequences, and ligands in a variety of formats.  This tool is launched as a stand-alone application using the Java Web Start protocol.
  • Map genomic position to protein. Mutations in a gene can have profound effects on the function of a protein. This analysis tool highlights the location of a gene location (i.e., the site of a SNP).
  • Explore sequence, structure, and related annotations. Protein Feature View provides a graphical summary of how sequence data corresponds to PDB entries. New options include visualization of sequence motifs and access to related organisms with the same gene name.
  • Access large structures.  "Large structures" (containing > 62 chains and/or 99999 ATOM lines) are represented as single files in PDBx/mmCIF and PDBML formats. These entries can be easily found (or omitted) using Advanced Search.  Corresponding tar files containing minimal/best effort files in PDB format that represent these entries can be accessed through individual Structure Summary pages and using the Download Tool.
  • Visualize structures quickly. JSmol (JavaScript Jmol), is now the default 3D viewer to improve usage speed.  The new program PV (Protein Viewer) is also offered as a powerful visualization tool. For large structures that have traditionally rendered slowly or were unable to load in 3D viewers, new features have been implemented to improve visualization.

See the What's New page for more new features and examples.


View of rubisco entry 4F0H oriented along symmetry axes (red tubes) using PV.



Join our Development Team in San Diego

28-Apr-2015

RCSB PDB is seeking exceptional developers

The RCSB PDB is seeking exceptional developers, and we know we're not alone in our search. So why choose to work with us? Our team values open discussion and contribution. Starting from your first day, you will shape software and services used by thousands of people around the world. Our organization can trace its lineage back to the 1970's, but we still operate like a start up. Have a great idea, let's hear it. Want to try a new technology, let's learn it. Want to write code at scale, let's do it. Everyone at our organization is passionate about what we do, and that is why we are leaders in our field. We want to hear from skilled Developers, people passionate about their craft and what they can bring to the field.

We are looking for two experienced Software Developers to join our team of agile Developers at the University of California, San Diego. By joining our team, a successful applicant would be able to contribute to a variety of projects ranging from:

  • Front end development using HTML, CSS, Javascript, JSP, and NodeJS
    • Our core business is our website and web services
  • Middleware development that leverages Memcached, Hibernate, and RabbitMQ
    • How we scale to meet tens of thousands of unique users every day
  • Back end development using Java, MySQL/MariaDB, and NoSQL solutions
    • Incorporating and adding value to the scientific community
    • Search using Apache Solr
    • Scalable solutions built on top of OpenStack, Hadoop, and Spark
  • Special projects

The RCSB Protein Data Bank (www.rcsb.org) is one of the world's leading biological databases with more than 300,000 unique users per month from over 160 countries. It enables access to the singular global archive of the three-dimensional structures of proteins and nucleic acids and is a key resource for the design of new medicines, biofuels, nanomaterials, and enables fundamental discoveries in biology and medicine.

For more requirements or to apply, please view the UCSD job page.



DNA Day 2015: April 25

21-Apr-2015

NHGRI's National DNA Day commemorates the completion of the Human Genome Project and the discovery of DNA's double helix. It's also a day for students, teachers, and the public to learn more about genetics and genomics.

Celebrate by:


Build PDB-101's paper model of DNA


Rutgers Day (April 27)

21-Apr-2015

Rutgers Day is a full day of discovery and lively activities that showcase the varied resources, departments, and people at the university. Learn about the Protein Data Bank, Health, and You with at the RCSB PDB booth in the Life Sciences area on Busch Campus. Explore biology at the molecular level by building virus and DNA models with your favorite candy.

Rutgers Day will take place from 10 a.m. - 4 p.m. rain or shine. Admission and parking are both free.



Education Corner: The Science of HIV

14-Apr-2015

Published quarterly in our Newsletter, each Education Corner feature offers an account of how members of the community use the PDB in education. Issues are archived online.

In the latest issue, Janet Iwasa describes her multimedia-rich website scienceofHIV.org. This project aims to use animated molecular visualizations to captivate, inform and educate diverse audiences.

Janet is also one of our esteemed judges for the 2015 High School Video Challenge. Submissions are due May 31; detailed information is available.

If you would like to submit an Education Corner column, please send an email to info@rcsb.org.



Spring Newsletter Published

07-Apr-2015

The Spring 2015 issue of the RCSB PDB Newsletter is now available.

Articles describe the new Molecular Machinery viewer, released just as the PDB reached 100,000 protein entries, large structures in the PDB, a paper describing the Chemical Component Dictionary, BioJava, and more.

The Education Corner highlights a new online resource for learning about HIV biology by Janet Iwasa.

RCSB PDB's Newsletter is published and archived online.  Sign up to receive electronic updates each quarter.



Take an Interactive Tour of the Protein Data Bank

31-Mar-2015

A new interactive viewer animates RCSB PDB's popular Molecular Machinery poster in 3D.

In 2014, Molecular Machinery: A Tour of the Protein Data Bank was published to celebrate the milestone 100,000 entries released in the PDB archive. Ninety-six structures illustrate the vast range of molecular shapes and sizes in the PDB. These structures are depicted relative to the cellular membrane and organized in categories related to function. A scale bar provides a sense of molecular size in nanometers.

The interactive view of Molecular Machinery lets users select a structure, access the entry in 3D using Protein Viewer (PV; requires WebGL enabled), read a brief summary of the molecule's biological role, and access the corresponding PDB entry and Molecule of the Month column.

Users can highlight structures in the Molecular Machinery viewer based on functional category. For instance, selecting "Blood Plasma" from the right menu highlights the structures shown that are involved with transporting nutrients and defending against injury.

The "Auto Mode" option will automatically launch a tour of the structures, highlighting the different categories of structures and the individual examples. The 3D view uses PV to rotate the molecule, use different depiction styles, and zoom in/out of the molecule. This mode can be used as a screensaver or as a kiosk display.

Users can access the Molecular Machinery Viewer from mm.rcsb.org and from the Educational Resources > Animations section of PDB-101. This viewer was designed and developed by Robert Lowe, Maria Voigt, and David S. Goodsell.

Molecular Machinery poster in 3D


Join the RCSB PDB Team

24-Mar-2015

RCSB PDB is looking for Web Developers at the UC San Diego site. Descriptions are available on our Careers page; applications should be submitted online. To become part of our team, please contact Dr. Peter Rose (peter.rose@rcsb.org).

The RCSB Protein Data Bank (www.rcsb.org) is one of the worldwide leading biological databases with more than 300,000 unique users per month from over 160 countries. It enables access to the singular global archive of the three-dimensional structures of proteins and nucleic acids and is a key resource for the design of new medicines, biofuels, nanomaterials, and enables fundamental discoveries in biology and medicine.

Join the RCSB PDB as a Web Developer.


Build 3D Paper Models of Biomolecules

24-Mar-2015

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

A collection of Paper Models are available to to build 3D models of DNA, transfer RNA (tRNA), dengue virus, green fluorescent protein (GFP), and the HIV capsid. Supporting materials are available, including a new video demonstrating how to create a model of tRNA.


Building a Paper Model of tRNA

Other educational materials at PDB-101 include the Molecule of the Month series, posters, animations, curriculum, and more.

PDB-101 also hosts resources to help students participate in the RCSB PDB's Video Challenge. High school students are challenged to tell a story of defeating, combating, and controlling the HIV pandemic at the molecular level using structures from the PDB.

An esteemed panel of judges will review the videos and make three awards: Judge's Choice, Viewer's Choice, and Service to the Community. Submission deadline is May 31, 2015.



Visit the San Diego Festival of Science and Engineering on March 22

17-Mar-2015

On Saturday March 22, visitors to the RCSB PDB booth at the San Diego Festival of Science and Engineering's EXPO DAY will learn about the basic building blocks of life by building a 3D model of DNA and a small zinc finger protein. They can also watch animations of 3D proteins and nucleic acids, and take home posters and other materials about these fascinating structures.

EXPO DAY is the grand-slam-science-finale to a week of big events at San Diego State University, Balboa Park and California State University San Marcos.

Tens of thousands of kids, families, scientists, engineers, educators, and other community members are expected to take part in this year's EXPO DAY, a free-to-the-community event! Visit sdsciencefestival.com for complete details.

Can't make it to San Diego? Build models of DNA and the dengue virus at home using these PDFs from PDB-101.



2015 High School Video Challenge

10-Mar-2015

In 2014, students created impressive videos illustrating the structural biology of HIV. This year, RCSB PDB is challenging students to tell a story of defeating, combating, and controlling the HIV pandemic at the molecular level using structures from the PDB.

An esteemed panel of judges will review the videos and make three awards: Judge's Choice, Viewer's Choice, and Service to the Community. The deadline for submission is May 31, 2015.

Many resources are offered to help students get started, including the new video Learn about HIV from the RCSB PDB. Visit PDB-101 for an overview, rules, HIV-related education materials, tutorials on making videos, and more.



New Publications

03-Mar-2015

Recent publications from the RCSB PDB and wwPDB include:

  • The RCSB Protein Data Bank: views of structural biology for basic and applied research and education (2015) Nucleic Acids Research 43(D1): D345-356 doi:10.1093/nar/gku1214
  • RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank (2015) Bioinformatics 31: 126-127 doi:10.1093/bioinformatics/btu596
  • Detection of Circular Permutations within Protein Structures using CE-CP (2014) Bioinformatics doi:10.1093/bioinformatics/btu823
  • The Chemical Component Dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank (2014) Bioinformatics doi:10.1093/bioinformatics/btu789
  • Small molecule annotation for the Protein Data Bank (2014) Database doi:10.1093/database/bau116

The full list of related publications is available at the RCSB PDB and wwPDB websites.



San Diego Science Olympiad Protein Modeling Results

03-Mar-2015

San Diego Science Olympiad Protein Modeling Results

On February 21, 49 teams from 20 San Diego County high schools built models of proteins involved in genome editing in the protein modeling event at the San Diego County Regional Division C competition.

The top scoring teams were:

  1. Team Soy from Canyon Crest Academy
  2. Team Bacon from Westview High School
  3. Team Calvin from Rancho Bernardo High School

RCSB PDB Annotator Michael Gao supervised the event, along with judges Lanfeng Wang and Wei Wang from University of California San Diego.

This year's protein modeling event was designed by MSOE and RCSB PDB, and highlights related Molecule of the Month columns as a resource. Protein modeling will be one of several events at Science Olympiad tournaments across the country and in the National events in May. Teams are recognized for their performance in individual events and in the overall tournament.

Related materials for protein modeling preparation are hosted by MSOE and RCSB PDB.



Exploring Structure Quality

24-Feb-2015

Structure Summary pages for X-ray crystal structures provide access to validation information based upon the recommendations of the wwPDB X-ray Validation Task Force:

  • A PDF report containing Ramachandran plots created using MolProbity. Ramachandran plots provide an independent method to evaluate the conformational quality of protein structures, and offer a visual representation of any outliers tabulated in the Validation Report PDF. For more information about MolProbity, see Chen et al. (2010) Acta Cryst D66:12-21.
  • The "slider" graphic displayed on the page gives an indication of the quality of the determined structure as compared with previously deposited PDB entries using several important global quality indicators
  • The full PDB Validation Report PDF, which contains the slider graphic and other information to provide an assessment of the quality of a structure and highlight specific concerns (visit the wwPDB for more information)

Previously, Ramachandran plots were located on the Structure Summary Geometry tab, which has been retired. Additional validation data and statistics are available from the Structure Summary Links tab, including reports by WHAT_CHECK and PROCHECK.



Ramachandran plots for entry for 1CBS

Ramachandran plots for entry 1cbs as created by MolProbity.



2015 High School Video Challenge Materials

17-Feb-2015



In 2014, students created impressive videos illustrating the structural biology of HIV. This year, RCSB PDB is challenging students to tell a story of defeating, combating, and controlling the HIV pandemic at the molecular level using structures from the PDB.

Videos will be judged by considered for three awards: Judge's Choice, Viewer's Choice, and Service to the Community.  The deadline for submission is May 31, 2015.

Many resources are offered to help students get started, including the new video Learn about HIV from the RCSB PDB. Visit PDB-101 for an overview, rules, HIV-related education materials, tutorials on making videos, and more.



BioJava 4.0.0 Released

10-Feb-2015

BioJava is an open source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and support manipulation of sequences and 3D structures.

Through BioJava, RCSB PDB releases algorithms and file parsers used at rcsb.org, including algorithms used in the protein Comparison Tool, some of the tracks of the Protein Feature View, and the algorithm for detecting symmetry in biological assemblies.

BioJava also contains a reference implementation for parsing and processing PDBx/mmCIF format data files.

A BioJava tutorial is available to help  facilitate rapid application development for bioinformatics.

BioJava: an open-source framework for bioinformatics in 2012.
Bioinformatics (2012) 28: 2693-2695.



NJ Science Olympiad Protein Modeling Results

03-Feb-2015

55 teams from high schools across New Jersey demonstrated their understanding of 3D protein structure at three regional Science Olympiad competitions held in January.

Students use Jmol to build a model on the day of the event.

Students use Jmol to build a model on the day of the event.

The models built by students are examples of proteins involved in genome editing. This year's event was designed by MSOE and RCSB PDB, and highlights related Molecule of the Month columns as a resource. Protein modeling will be one of several events at Science Olympiad tournaments across the country and in the National events in May. Teams are recognized for their performance in individual events and in the overall tournament.

The top scoring teams in the New Jersey Science Olympiad regional protein modeling events were

Northern (NJIT, Jan 15, 2015)

  1. Al-Ghazaly HS
  2. Montville Township HS
  3. Biotechnology HS
  4. Morris Hills HS
  5. Parsippany Hills HS
  6. Millburn HS

Central (UCC, Jan 7, 2015)

  1. West Windsor-Plainsboro HS North - II
  2. South Brunswick HS - II
  3. South Brunswick HS - I
  4. Randolph HS - I
  5. Union County Vocational Technical Schools - I
  6. JP Stevens HS - I

Southern (CCC, Jan 15, 2015)

  1. Montgomery HS - II
  2. Princeton HS - I
  3. Montgomery HS - I
  4. New Providence HS - II
  5. Princeton HS - II
  6. Lawrence HS
Science Olympiad at UCSD campus

RCSB PDB will also participate in the San Diego Regional event on February 21, and recently hosted a protein modeling workshop at UCSD.

Science Olympiad Judges

Judges Luigi Di Costanzo, Shuchismita Dutta (also an event creator), and Yuhe Liang

Many thanks to the RCSB PDB judges in NJ (Luigi Di Costanzo, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, Brian Hudson, Yuhe Liang, Ezra Peisach, Chenghua Shao, Lihua Tan, Christine Zardecki, and Marina Zhuravleva), the NJ Science Olympiad organizers and volunteers, and the host colleges (Camden County, Union County, and NJIT).

We look forward to seeing the teams at the NJ state finals in March! Related materials for protein modeling preparation are hosted by MSOE and RCSB PDB.



wwPDB Deposition Tool Replaces ADIT for Crystal Structures

27-Jan-2015

wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of a new Deposition and Annotation System. Using this system, more than 4,200 structures have been deposited and annotated, and >1,700 structures released in the archive.

Features of the new system include use of the PDBx/mmCIF data format, which produces more uniform data; the ability to replace data files pre- and post-deposition; enhanced communication; improved annotation; and geometric and experimental data checking based on recommendations from expert task forces. Detailed information and video tutorials are available.

As a result of this successful release, ADIT has been retired at RCSB PDB and PDBj for new depositions of structures determined from X-ray crystallographic experiments. Existing, in-progress ADIT sessions of X-ray crystallographic structures can be accessed until July 19, 2015.

ADIT will continue to accept depositions from other experimental methods. Deposition tools for NMR and 3DEM are being developed by the wwPDB.

Questions and comments should be sent to info@wwpdb.org.



RCSB PDB Mobile for iOS and Android Update

20-Jan-2015

RCSB PDB Mobile is a universal app that enables the general public, researchers and scholars to search the PDB and visualize protein structures using mobile devices.

Freely available for the iPhone/iPod/iPad and Android (2.3.3 and above), RCSB PDB Mobile can be used to search the entire PDB database, view the latest released structures, access MyPDB accounts, and view the entire catalog of Molecule of the Month articles.

A program update has been released at the Apple Store and Google play which includes the latest Molecule of the Month article and bug fixes for recent indexing issues.

Known issues will be listed on the RCSB PDB Mobile support page. Currently, the molecular viewer used in the app (NDKmol) cannot support large structures with more than 62 chains and/or 99,999 atoms, and cannot be used on Android 5.0 (Lollipop).  The app will be updated as new versions are made available.

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank
(2014) Bioinformatics doi:10.1093/bioinformatics/btu596





Winter Newsletter Published

13-Jan-2015

Winter 2015 Newsletter Published

The Winter 2015 issue of the RCSB PDB Newsletter is now available.

Articles explore 2014 statistics and highlights, large structures in the PDB, 15 years of the Molecule of the Month, and more.

This issue's Education Corner describes how teachers have Mentored High School Students for the RCSB PDB HIV Video Challenge.

RCSB PDB's Newsletter is published and archived online. Sign up to receive electronic updates each quarter.



New Calendar Celebrates 15th Anniversary of Molecule of the Month

06-Jan-2015

15th Anniversary of Molecule of the Month

In January 2000, the Molecule of the Month was launched with a feature on myoglobin, the first structure determined using X-ray crystallography.  Since then, 180 Molecule of the Month articles have explored the structure and function of PDB macromolecules from AAA+ proteases to Zinc fingers. These articles are one of the most popular features of the RCSB PDB website and are utilized by classrooms around the world.

Authored and illustrated by David S. Goodsell, Molecule of the Month features have grown over the years to include curated, interactive views, discussion topics, and links to specific examples. The carefully composed illustrations, available free for use as high resolution images, have been reproduced and used in countless educational resources.  These unique pictures of molecular machines provided both inspiration and content for the Art of Science traveling exhibit.

Through the years, Molecule of the Month features have become tightly integrated with other RCSB PDB initiatives. Many posters, paper models, and animations have been built using these features.  The articles have also led to the creation of the Structural View of Biology browser, which offers top-down contextual exploration of the PDB. January's focus on Cascade and CRISPR will be used in this year's protein modeling event in the Science Olympiad.

To celebrate this special anniversary, we have assembled an online PDF calendar for 2015 that features a small selection of the many molecular highlights of the past 15 years.



Video Challenge for High School Students

06-Jan-2015

15th Anniversary of Molecule of the Month

In 2014, students created impressive videos illustrating the structural biology of HIV. This year, RCSB PDB is challenging students to tell a story of defeating, combating, and controlling the HIV pandemic at the molecular level using structures from the PDB.

Videos will be judged by considered for three awards: Judge's Choice, Viewer's Choice, and Service to the Community.  The deadline for submission is May 31, 2015.

RCSB PDB offers many resources to help students get started. Visit PDB-101 for an overview, rules, HIV-related education materials, tutorials on making videos, and more.



2015 Index

Earlier news is available and is archived in the RCSB PDB newsletters.