News 2017
Donate Today to Support the PDB's Spirit of Openness, Cooperation and Education
09/19/2017
Head Back to School with PDB-101
09/12/2017
Poster Prize Awarded at ISMB
08/15/2017
Torres Takes Poster Prize for a Second Time at ACA
08/08/2017
Summer Newsletter Published
07/25/2017
Annual Report Published
07/18/2017
New Video: How Enzymes Work
06/26/2017
Guide to Understanding PDB Data: Small Molecules
06/20/2017
Award-Winning Structural Biology/Diabetes Videos
06/13/2017
Vote Now for the Video Viewer's Choice Award
05/30/2017
Learning Structural Biology in Virtual Reality
05/09/2017
Spring Newsletter Published
04/11/2017
Zika Illustration Named People’s Choice
04/04/2017
See the Art of Science at Rutgers' S.T.E.A.M. Women's Empowerment Conference on March 25
03/23/2017
PDB-101 is "Best of the Web"
03/21/2017
Enter the 2017 Video Challenge
02/21/2017
Molecular Origami: Build 3D models of Zika virus
01/31/2017
Winter Newsletter Published
01/10/2017
2016 FASEB BioArt Winner
01/03/2017

Donate Today to Support the PDB's Spirit of Openness, Cooperation and Education

09/19/2017

The wwPDB Foundation raises funds from Individual and Corporate sponsors in support of the outreach activities of the wwPDB crucial to the future of the PDB archive, including workshops, symposia, and advisory meetings.

Corporate sponsors are acknowledged on the Foundation website, with opportunities to post job listings and use the Foundation logo on marketing materials.

Individual sponsors ($100 or more for professionals, $25 or more for students) are acknowledged online and with a special gift.

To support the wwPDB Foundation in 2017, please contact Christine Zardecki or donate online via PayPal (no account needed).

RCSB PDB News ImageIndividual sponsors will receive this hemoglobin lapel pin.


Head Back to School with PDB-101

09/12/2017

PDB-101 is RCSB PDB’s online portal for teachers, students, and the general public that promotes exploration in the world of proteins and nucleic acids. Learning about the diverse shapes and functions of these biological macromolecules helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy.

This website ("101", as in an entry level course) presents introductory materials that introduce beginners to the structures of proteins and nucleic acids contained in the PDB archive. Resources for extended learning are also provided.

PDB-101 offers curricular materials, templates to create 3D paper models, Molecule of the Month articles, and other materials developed by RCSB PDB.

Users can search the website for related materials using molecule name or keyword. The Browse option can be used to explore available PDB-101 resources organized by topics such as the immune system and renewable energy.

PDB101.rcsb.org is updated with news and features regularly.

RCSB PDB News ImageImage of hemoglobin from the Geis Digital Archive. Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.
RCSB PDB News ImageLearn why the proteins called enzymes are essential to life on earth, and observe an example catalysis mechanism in this new video.


Poster Prize Awarded at ISMB

08/15/2017

At this year's meeting of the 2017 Intelligent Systems for Molecular Biology (ISMB) Conference, the award went to Jinwoo Leem for Next generation structure-based antibody drug design with ABodyBuilder and PEARS (Jinwoo Leem, Guy Georges, Jiye Shi, Charlotte M. Deane, University of Oxford).

Many thanks to Co-Chairs Casey Greene (University of Pennsylvania) and (Arjun Krishnan, Michigan State University, the entire Posters Committee, and Steven Leard (ISMB).

All 2017 awardees will be listed on the RCSB PDB website and will receive an educational book.

RCSB PDB News ImageJinwoo Leem


Torres Takes Poster Prize for a Second Time at ACA

08/08/2017

At this year's meeting of the American Crystallographic Association, the award went to Miguel Torres for Crystallization and preliminary structural studies of an aldo-keto reductase from opium poppy (Miguel Torres, Mehran Dastmalchi, Peter Facchini, and Kenneth Ng, University of Calgary).

Many thanks to judges Thomas Koetzle, Bruce Noll (Bruker), Przemyslaw Porebski (University of Virginia), and Peter Müller (MIT).

All 2017 awardees will be listed on the RCSB PDB website and will receive an educational book.

This is the second year in a row that Miguel has been awarded this Prize. Last year, he was recognized for his work Crystallographic Structures of Pavine N-methyltrasferase Complexes Reveal New Insights into Substrate Recognition and Catalytic Mechanism.


Summer Newsletter Published

07/25/2017

The Summer 2017 issue of the RCSB PDB Newsletter is now online.

This issue celebrates Helen Berman’s ACA award, describes upcoming changes to the FTP archive, and shows how to access structural variations using PDBFlex data.

In the Education Corner, Molecule of the Month creator David Goodsell asks readers to Get Excited, Be Critical and describes his new book on Atomic Evidence: Seeing the Molecular Basis of Life.

RCSB PDB's Newsletter is published and archived online.


Annual Report Published

07/18/2017

Download the 2016 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

This review highlights many RCSB PDB accomplishments, including educational materials focused on Diabetes and powerful 3D visualization tools.

wwPDB efforts, including deposition statistics and the OneDep system for deposition, validation, and biocuration, are also highlighted.

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

RCSB PDB News ImageZika virus is shown in cross section at center left. Visible on the periphery are envelope proteins (pink) and membrane proteins (magenta) embedded in a lipid membrane (light purple). Within the interior of the virus, the RNA genome (yellow) is associated with capsid proteins (orange). Two viruses are shown interacting with cell surface receptors (green) and are surrounded by blood plasma proteins outside the cell. This painting was recognized by the National Science Foundation (NSF) and Popular Science as one of the best science images of the year and selected as the “People’s Choice” in the illustration category for the 2017 Vizzies.


New Video: How Enzymes Work

06/26/2017

RCSB PDB News Image

Every second inside every living cell, thousands of chemical reactions are taking place. These reactions constitute the essential tasks of life such as metabolism, protein synthesis, cell renewal and growth.

Learn how the proteins called enzymes work to maintain the rate of these reactions at a life-sustaining level in this new video hosted by PDB-101.

Explore the PDB-101 Browser to learn more about enzymes.


Guide to Understanding PDB Data: Small Molecules

06/20/2017

The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world. This can make it both exciting and challenging to use the database in research and education.

PDB-101's Guide to Understanding PDB Data was created to help users navigate through the contents of the archive without having a detailed background in structural biology.

Topics cover biological assemblies, molecular graphics programs, R-value and R-free, and more.

A new chapter has been added to help users examine the Small Molecule Ligands are represented in the PDB archive. Topics in this article include:

  • General Overview
  • Representation of Ligands in Entry Files
  • Free Ligands vs. Ligands in Polymers
  • Biologically Interesting Molecules
  • Electron Density Visualization
  • Ideal and Model Ligand Representations


Award-Winning Structural Biology/Diabetes Videos

06/13/2017

For the fourth year, RCSB PDB invited high school students to tell molecular stories in video. This year's challenge focused on the molecular view of the diabetes treatment and management. The challenge entries (all available online) demonstrate a wide variety of topics with many creative story-telling approaches.

Our panel of expert judges scored the videos based on scientific content (40%), creativity (20%), overall impact (20%), entertainment value (10%), and production quality (10%). In addition, the general public voted for the Viewer's Choice Award.

Congratulations to the 2017 Winners (which can be viewed online):

  • First Place: Insulin: From Bacteria To You By Andrew Ma, George Song, and Anirudh Srikanth of West Windsor-Plainsboro High School South in Princeton Junction, NJ (Team Advisor: Matthew Foret)
  • Second Place: Metformin and DPP 4 Inhibitors Take the DIE out of Type 2 Diabetes By Julie Chaimowitz, Fiona Lu, Lori Mohs, and Amy Ni of East Brunswick High School, East Brunswick, NJ (Team Advisor: Louise Jasko)
  • Third Place: Sugary Solutions: An In Depth Look at the Treatment of Type 2 Diabetes By Audrey Guo and Anna Shi of West Windsor-Plainsboro High School South, Princeton Junction, NJ (Team Advisor: Meenakshi Bhattacharya)
  • Viewer's Choice: Type 2 Diabetes: Meet It Beat It By Kerwin Chen, Raisa Khuda, and Tasnuba Sukanna of Stuyvesant High School in New York, NY (Team Advisor: Gilbert Papagayo)

Many thanks to the expert judges, students, teachers, parents, judges, and voters who made this exciting competition happen!


Vote Now for the Video Viewer's Choice Award

05/30/2017

RCSB PDB recently challenged high school students to create videos telling the story of diabetes treatment and management. Watch the challenge entries online and cast your vote now for your favorite video.

Voting for the Viewers Choice Award is now open until June 6th 12:59 EST. Winners will be announced at PDB-101 and rcsb.org on June 13, 2017.


Learning Structural Biology in Virtual Reality

05/09/2017

RCSB PDB News Image

The latest Education Corner describes Learning in Virtual Reality: Revolutionizing education with Autodesk's Molecule Viewer. This viewer is a free, online 3D visualization tool for modern scientists and learners to explore, share, and present molecular data. It was recently used to curate an present a structural biology symposium on the retinal protein world.

Published quarterly in our Newsletter, each Education Corner offers an account of how members of the community use the PDB to educate students. If you would like to submit an Education Corner column, please send an email to info@rcsb.org.

The spring RCSB PDB Newsletter also includes the report of the Global Life Sciences Data Resources (GLSDR) Working Group, plans for updating all PDBx/mmCIF model files to the V5 version of the PDBx/mmCIF dictionary, and open Postdoctoral Fellow positions at RCSB PDB at UCSD. Recent PDB-101 highlights are presented, including a 2017 NSF/Popular Science Vizzie Award, 2016 FASEB BioArt Award, and recognition by Genetic Engineering & Biotechnology News as Best of the Web.

RCSB PDB's Newsletter is published and archived online.


Spring Newsletter Published

04/11/2017

The Spring 2017 issue of the RCSB PDB Newsletter is now online.

Topics include the report of the Global Life Sciences Data Resources (GLSDR) Working Group, plans for updating all PDBx/mmCIF model files to the V5 version of the PDBx/mmCIF dictionary, and open Postdoctoral Fellow positions at RCSB PDB at UCSD. Recent PDB-101 highlights are presented, including a 2017 NSF/Popular Science Vizzie Award, 2016 FASEB BioArt Award, and recognition by Genetic Engineering & Biotechnology News as "Best of the Web."

In the Education Corner, Merry Wang (Autodesk Research) describes Learning in Virtual Reality: Revolutionizing education with Autodesk's Molecule Viewer.

RCSB PDB's Newsletter is published and archived online.


Zika Illustration Named People’s Choice

04/04/2017

Since 2003, the Vizzies Challenge has recognized visualizations of scientific data that are “exemplars of information made beautiful.”

At the 2017 Vizzies, David Goodsell's painting for the Molecule of the Month was recognized by the National Science Foundation (NSF) and Popular Science as one of the best science images of the year and selected as the “People’s Choice” in the category of illustration.

The image also appeared on the cover of Wing Beats and Cell Host & Microbe, and inspired other PDB-101 materials available for download, including Zika paper models and a coloring book.


See the Art of Science at Rutgers' S.T.E.A.M. Women's Empowerment Conference on March 25

03/23/2017

RCSB PDB News ImageThe Art of Science uses the context of a community art gallery to introduce new audiences to to the beauty of structural biology.

RCSB PDB’s traveling art exhibit The Art of Science will be featured at the Dr. Jewel Plummer Cobb S.T.E.A.M. Women’s Empowerment Conference entitled Nevertheless, She Persisted on March 25th at the Rutgers Busch Student Center in Piscataway. This event is hosted by the Division of Student Affairs and #stemHERstoryRU.

Dr. Jewel Plummer Cobb was an influential educator, trailblazer and scientist who served as the sixth Dean of Douglass at Rutgers from 1976 to 1981. Dr. Cobb passed away on New Year’s Day, 2017, at the age of 92, in Maplewood, NJ.

S.T.E.A.M. Women’s Empowerment Conference is a forum where individuals will be inspired to take personal responsibility in owning and embracing their story and identity. Admission is free; registration is online.


PDB-101 is "Best of the Web"

03/21/2017

Genetic Engineering & Biotechnology News recently highlighted PDB-101 as Best of the Web, recognizing the website's beautiful protein structures and wealth of educational resources.

PDB-101 is an online portal developed by RCSB PDB for teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids. PDB-101 features support learning about the diverse shapes and functions of these biological macromolecules and their relationship to biomedicine and agriculture, from protein synthesis to health and disease to biological energy.

These resources are made freely available thanks to support from the National Science Foundation (DBI-1338415), the National Institutes of Health, and the US Department of Energy.

RCSB PDB News ImageInteractive Molecular Machinery animation available from PDB-101.


Enter the 2017 Video Challenge

02/21/2017

RCSB PDB News Image

For the fourth year, RCSB PDB invites high school students across the USA to create short videos that tell a molecular story of health and disease. This year’s focus is the Molecular View of Diabetes Treatment and Management. To get started, teams are encouraged to use PDB-101 resources related to diabetes, diabetes treatments, and molecular visualization.

Videos may be submitted from March 7, 2017– May 22, 2017. Award winners will be announced on June 13, 2017.

For more information, sign up for the Video Challenge Monthly Newsletter and visit the challenge webpage at PDB-101.


Molecular Origami: Build 3D models of Zika virus

01/31/2017

Zika virus infects people around the globe. For most, the virus causes a mild illness that is quickly fought off by the immune system. But a connection between Zika infection in pregnant women and birth defects has underscored the need to find ways to fight the disease. Zika is spread by mosquitos, so our primary defense is to remove breeding sites and to take measures to avoid being bitten. There are a few examples of the Zika virus and related structures available in the PDB archive. Public availability of these atomic coordinates to medical researchers worldwide will accelerate new antiviral drug and vaccine development.

To build paper models of the Zika virus, download and print the template PDFs (Zika Virus/5ire and Zika Virus with antibodies/5h37).

RCSB PDB News ImageBuild a paper model of Zika virus (PDB entry 5ire)
RCSB PDB News ImagePaper model of Zika virus with neutralizing antibodies (PDB entry 5h37)
RCSB PDB News ImageCut out the structure along the dashed lines, and fold along the solid lines. Then tape or glue the flaps into place to form the viral icosahedron.

Use the PDB-101 Browser to explore more resources and articles about Zika and other viruses.


Winter Newsletter Published

01/10/2017

The Winter 2017 issue of the RCSB PDB Newsletter is now online.

Read about 2016 milestones and a review of recently-added website tools and features.

In the Education Corner, Rebecca Alford and Jeffrey Gray (Johns Hopkins) describe the Rosetta Commons summer Research Experience for Undergraduates (REU). Interested in applying? Submissions are due February 1, 2017.

RCSB PDB's Newsletter is published and archived online.


2016 FASEB BioArt Winner

01/03/2017

Video stills of three HIV enzymes are among the 2016 Winners of FASEB's BioArt Competition. This year’s 10 winning images and three videos represent a wide range of research in the biomedical and life sciences, from technology that may aid in recovery from spinal cord injury to a portrait of the New York City skyline “printed” in yeast.

Winning entries were unveiled on FASEB’s website and will be exhibited at the National Institutes of Health.

The stills are from a new molecular animation available at PDB-101 that illustrates A Molecular View of HIV Therapy.

RCSB PDB News ImageVideo stills from the animation A Molecular View of HIV Therapy by Maria Voigt and David S. Goodsell


Past news and events have been reported at the RCSB PDB website and past Newsletters.