News 2017
New Video Answers "What is a Protein?"
11/21/2017
Postdocs and Developers: Join Our Team
11/14/2017
Highlighting Structural Biology
11/07/2017
PDB Trends: Expanding Boundaries of Complexity with 3DEM
10/31/2017
Color the Diverse 3D Shapes Studied by Crystallographers
10/24/2017
Fall Newsletter Published
10/10/2017
User Survey: Tell RCSB PDB About Your Interests
10/01/2017
Get Excited, Be Critical
09/26/2017
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

New Video Answers "What is a Protein?"

11/21/2017

In 2013, PDB-101 released its first molecular animation, What is a Protein?. Since then, that video has been viewed more than 450,000 times.

Since then, PDB-101 has published many more videos and animations, including How Enzymes Work and A Molecular View of HIV Therapy.

Building upon the success of these new features, What is a Protein? has been updated and improved for 2017. Watch it now at PDB-101.

RCSB PDB News Image
RCSB PDB News Image
RCSB PDB News Image

A related PDF Flyer is also available for download from PDB-101.


Postdocs and Developers: Join Our Team

11/14/2017

RCSB PDB News ImageRCSB PDB is looking for Scientific Software Developers and Postdoctoral Fellows in to join the Development Team at UC San Diego.

We are looking for talented and highly motivated Scientific Software Developers and Postdoctoral Fellows to join our multidisciplinary development team.

The Challenge: Develop innovative analysis, integration, query, and visualization tools for 3D biomolecular structures to help accelerate research and training in biology, medicine, and related disciplines. In these projects, we employ the latest advances in computer science to develop highly interactive features and scalable services and workflows. This is a unique opportunity to engage in leading edge research, development, and outreach activities of the RCSB PDB with worldwide impact. For more, visit our Careers page or Contact Us with questions.

RCSB PDB News ImageRCSB PDB Development Team members are located at UC San Diego and Rutgers, The State University of New Jersey.


Highlighting Structural Biology

11/07/2017

Each structure in the Protein Data Bank contributes to our greater understanding of biology and medicine.

Structural Biology Highlights hosted at PDB-101 explore some of the structures made possible by the Protein Structure Initiative (PSI) supported by the NIGMS from 2000-2015.

PSI researchers focused on accelerating discovery in structural genomics and contributing to understanding biological function. As a result, PSI efforts developed new technologies and methods that improved the process of protein structure determination and prediction.

Over its 15-year period, nearly 7000 PDB structures were determined. Many of these structural advances are highlighted in these Structural Biology Highlight articles (formerly called Featured Systems).

These articles, written by Molecule of the Month creator David S. Goodsell, originally appeared at the Structural Biology Knowledgebase website (SBKB.org) that served as an information portal for PSI structures, theoretical models, technologies, and related information.

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. M. J. Gabanyi, P. D. Adams, K. Arnold, L. Bordoli, L. G. Carter, J. Flippen-Andersen, L. Gifford, J. Haas, A. Kouranov, W. A. McLaughlin, D. I. Micallef, W. Minor, R. Shah, T. Schwede, Y. P. Tao, J. D. Westbrook, M. Zimmerman, H. M. Berman. (2011) J Struct Funct Genomics 12: 45-54.


PDB Trends: Expanding Boundaries of Complexity with 3DEM

10/31/2017

3D electron microscopy (3DEM) is revolutionizing the field of structural biology. Atomic structures of biomolecules are now being determined by 3DEM, due to recent advances in several key technologies, including methods for sample preservation, vastly improved microscopy optics and detectors, and novel methods for structure solution with advanced computing. Researchers are also taking an integrative approach, determining atomic structures of subunits with X-ray crystallography and NMR spectroscopy, then using them to build a large assembly based on data from 3DEM. 3DEM is proving to be a perfect complement to X-ray and NMR techniques, since 3DEM is most effective on large, complex assemblies, which are typically difficult to study by other methods, and does not require large quantities of material, homogeneous samples, or crystallization.

Structures from 3DEM are made publicly available in the PDB archive to help further scientific research and education. The PDB released its first 3DEM entry in 1991, the ground-breaking structure of bacteriorhodopsin. Since then, more than 1700 3DEM structures have been made available in the PDB archive, with more than 1000 released from 2015-2017.

A new flyer highlights Nobel Prize-winning research in cryo-electron microscopy and other PDB structures determined using 3DEM. Download the PDF or explore the structures at PDB-101.

RCSB PDB News Image
RCSB PDB News Image


Color the Diverse 3D Shapes Studied by Crystallographers

10/24/2017

RCSB PDB News ImageThis coloring book illustrates the crystallographic pipeline.
RCSB PDB News ImageStructures from the CSD and PDB are highlighted.

Crystallography is the study of atomic and molecular structure. Crystallographers want to know how the atoms in a material are arranged in order to understand the relationship between atomic structure and properties of these materials. They work in many disciplines, including chemistry, geology, biology, materials science, metallurgy and physics. Crystallographers study diverse substances, from living cells to superconductors, from protein molecules to ceramics.

This book focuses on the diverse 3D shapes and functions of biological molecules studied by crystallography. Crystallographers make these 3D structure data publicly available in online resources like the Protein Data Bank and the Cambridge Structural Database. This broad access helps researchers, educators, and students around the world better understand biology and medicine.

Crystallographers also work together in strong communities. The American Crystallographic Association (ACA) is a non-profit, scientific organization that promotes interactions among scientists who study the structure of matter at atomic (or near atomic) resolution.

This coloring book was created with support from the ACA. Download the booklet or individual pages from PDB-101.

Bulk copies may be requested for use in outreach and education. Order today--limited quantities are available.


Fall Newsletter Published

10/10/2017

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

This issue introduces the 2017 User Survey; PDB-Dev, the prototype system for Integrative/Hybrid structural models, and improved text searching.

The Education Corner reports on an educational symposium held at the 2017 IUCr meeting focused on Structural Databases as Teaching Tools.

RCSB PDB's Newsletter is published and archived online.


User Survey: Tell RCSB PDB About Your Interests

10/01/2017

RCSB PDB News Image

RCSB PDB wants to learn more about our users worldwide. Please take this brief survey and be entered into a drawing for a poster, 2018 calendar, or Zika model.

The results of this survey will help us better understand RCSB PDB users and interests.

All survey responses are greatly appreciated!

RCSB PDB News ImageHow Do Drugs Work? Printed poster is 26 x 38” Also available as a PDB-101 PDF.
RCSB PDB News ImagePrinted model shows the Zika virus with neutralizing antibodies. Also available as a PDB-101 PDF.
RCSB PDB News ImageRCSB PDB's printed 2018 calendar will highlight PDB structures related to antimicrobial resistance.


Get Excited, Be Critical

09/26/2017

In the latest Education Corner, David Goodsell asks readers to Get Excited, Be Critical when storytelling and describes his new book on Atomic Evidence: Seeing the Molecular Basis of Life. David is the author of the Molecule of the Month, a series at the RCSB Protein Data Bank that presents the structure and function of a new molecule each month, and several illustrated books on biological molecules, their diverse roles within living cells, and the growing connections between biology and nanotechnology.

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 Summer 2017 issue of the RCSB PDB Newsletter also celebrates Director Emerita Helen Berman’s ACA award, describes upcoming changes to the FTP archive, and shows how to access structural variations using PDBFlex data.

RCSB PDB's Newsletter is published and archived online.

RCSB PDB News ImageEvolution of cytochrome c can be observed using structures in the PDB archive, by hypothesizing that proteins that are most similar in sequence correspond to organisms that are most closely related. In this illustration, the human enzyme is in red, amino acids that are different in other organisms are colored pink if they are chemically similar, and white if they are completely different. Based on this information, you can build a family tree such as the one shown below the structures. Image from the book Atomic Evidence, using PDB entries 3zcf, 2i8b, 1hrc, 1cyc and 2i8b)


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.