Year 2016 News Articles

Access to wwPDB and RCSB PDB websites

21-Jun-2016

The mission of the Worldwide Protein Data Bank (wwPDB) is to maintain a single Protein Data Bank archive of macromolecular structural data that is freely and publicly available to the global community.  The wwPDB website links to member websites, deposition resources, and information about data dictionaries and file formats.  Starting June 30, this website can be accessed via wwPDB.org or PDB.org.

RCSB PDB resources will continue to be hosted at RCSB.org. No changes need to be made to bookmarked RCSB PDB resources.



Award-Winning Videos about Structural Biology and Diabetes

14-Jun-2016

2016 Video Challenge Awards

For the third year in a row, the RCSB PDB invited high school students to create short videos that tell a molecular story. This year's challenge focused on sugar metabolism and its complications leading to diabetes. The 82 challenge entries available online show 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 (10%), originality of concept (10%), entertainment value (10%), and production quality (10%). In addition, the viewers were invited to vote for the Viewer's Choice Award.

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


Congratulations to the 2016 Winners:

Judge's Award First Place: Sweet Signals: Insulin and Glucagon in Diabetes

By Alexis D'Souza, Sruthi Katakam, and Nithilam Subbaian of West Windsor-Plainsboro High School South in Princeton Junction, NJ (Team Advisor: Matthew Foret)


Judge's Award Second Place: A Bird's Eye View of Pathways in You - Structural View of Insulin and Glucagon

By Gabby Stryker and Posy Stoller from La Jolla Country Day School, LaJolla, CA (Team Advisor: Susan Domanico)


Judge's Award Third Place: Types of Diabetes

By Alice Liu, Shayan Gupta, and Himali Patel of East Brunswick High School in East Brunswick, NJ (Team Advisor: Anne Sanelli)


Viewer's Choice Award: It's Me, You, and Glucose

By Amber Figueroa, Kimberly Gardner, Shane Meledathu, and Emily Payamps of McNair Academic High School in Jersey City, NJ (Team Advisor: Chumki Gupta)



Join our Development Team in San Diego

07-Jun-2016


We are looking for a talented and highly motivated Postdoctoral Fellow to join our multidisciplinary team at UC San Diego.

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 this project, we will employ the latest advances in computer science to develop highly interactive features and scalable services and workflows for the RCSB PDB website.

This position is a unique opportunity to engage in leading edge research, development, and outreach activities of the RCSB PDB with worldwide impact.

Qualifications: Ph.D. in one or more of the following research areas

  • Structural Bioinformatics, or related field with a focus on software development
  • Structural Biology with a focus on software development
  • Computer Science with a focus on bioinformatics algorithm development or visualization

Demonstrated proficiency in a high-level programming language, such as Java or Python and experience with state of the art software development tools. Experience with front-end programming languages (JavaScript) and libraries. Strong skills in problem solving and algorithm design are required. High productivity demonstrated by publications and contributions to open source software projects. Experience in the development of modern web applications, user interface design, or scientific visualization is a plus. Excellent written and oral communication skills.

Note, this position is reviewed annually on the basis of performance and can be renewed.

Our Environment:

The Structural Bioinformatics Group at the San Diego Supercomputer Center (SDSC) is involved in research and development activities centered around 3D structures of proteins and nucleic acids, the integration of structural data with other domains such as Medicine, Genomics, Biology, Drug Discovery, and the development of scalable solution to Big Data problems in Structural Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB) west-coast operations. The RCSB PDB represents the preeminent source of experimentally determined macromolecular structure information for research and teaching in biology, biological chemistry, and medicine. With over 300,000 unique users from over 160 countries around the world, the RCSB PDB is one of the leading worldwide Biological Databases. Our group is also involved in the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.

As an Organized Research Unit of UC San Diego, SDSC is a world leader in data-intensive computing and cyber infrastructure, providing resources, services, and expertise to the national research community, including industry and academia.

To apply, please send cover letter and resume to Dr. Peter Rose at peter.rose@rcsb.org.



Vote Now!

31-May-2016

RCSB PDB recently challenged high school students to create short videos that tell a story about structural biology and diabetes.

View the videos online, and then cast your vote for the Viewer's Choice Award. Voting will be open from June 1st 9:00am EST until June 7th 12:59 EST at PDB-101

Award winners will be announced at PDB-101 and rcsb.org on June 14, 2016.



Join the Sequence-Structure Hackathon at ISMB Orlando 2016

24-May-2016

From the evening of July 8th to the morning of July 11th, NCBI and the RCSB PDB will assist the International Society for Computational Biology (ISCB) in hosting a sequence-structure hackathon focused on integrating protein structure information and viewers with genomic sequence and variants, pharmacogenomic binding, and general laboratory practice. To apply for this hackathon, complete this form (approximately 10 minutes to complete). Applications are due June 10th, 2016 by 5 pm ET.

This event is for students, postdocs and investigators or other researchers already engaged in the use of JavaScript-based viewers for protein structure visualization and/or genome/gene/protein sequence browsers. It is open to anyone selected for the hackathon, and registered for the ISMB 2016 meeting.

Working groups of 5-6 individuals will be formed into five or six teams. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. The potential subjects for this iteration are:

  • Presenting data to and from JavaScript-viewable protein structures,
  • Simplified structure diagrams,
  • A digital notebook for structural biologists,
  • And pharmacogenomic association in conserved binding sites*.

* Some of the projects will build on APIs feeding data to or extracting data from viewers, so applicants need not be working on JavaScript viewers per se. For example, there is an opportunity to interface existing applications and libraries using any programming language with the Macromolecule Transmission Format (MMTF) for ultrafast access, parsing, and processing of PDB structures.

Please see the application for specific team projects.

Organization

After a brief organizational session, teams will spend three days analyzing a challenging set of scientific problems related to a group of datasets. Participants will analyze and combine datasets in order to work on these problems.

Datasets

Datasets will come from the public repositories housed at the NCBI, PDB and elsewhere.

Products

All pipelines and other scripts, software and programs generated in this course will be added to a public GitHub repository designed for that purpose. A manuscript outlining the design and usage of the software tools constructed by each team will be submitted to an appropriate journal.

Application

To apply, complete this form (approximately 10 minutes to complete). Applications are due June 1st, 2016 by 5 pm ET. Participants will be selected from a pool of applicants based on the experience and motivation they provide on the form. Prior participants and applicants are especially encouraged to reapply. The first round of accepted applicants will be notified on June 3rd by 5 pm ET, and have until June 6th at noon to confirm their participation.

If you confirm, please make sure it is highly likely you can attend, as confirming and not attending bars other data scientists from attending this event. We understand this hackathon is going on during an information-dense scientific meeting, so we ask that attendees attend at least part of three out of five scientific sessions in the draft daily schedule. Please include a monitored email address, in case there are follow-up questions.

Note: Participants will need to bring their own laptop to this program. A working knowledge of scripting (e.g., Shell, Python) is necessary to be successful in this event. Knowledge of JavaScript will be particularly helpful in this event. Applicants must be willing to commit to all three days of the event. No financial support for travel, lodging or meals is available for this event. Also note that the event may extend into the evening hours on Friday and/or Saturday. Please make any necessary arrangements to accommodate this possibility. Awards for achievements like "Most Prolific Code Development" will be given at the ISCB awards ceremony on Tuesday.

Please contact ben.busby@nih.gov with any questions.



Contact Customer Services with Questions and Feedback

17-May-2016

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.

Related resources include Help Topics for a variety of RCSB PDB services, a Website FAQ, a Glossary of Terms, a Browser Check to see if the web browser used is compatible with all rcsb.org services, and a Service Status page that indicates if all services are up and running.

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

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


Video Challenge Deadline: May 29

10-May-2016

For the third year, RCSB PDB is inviting high school students to create short videos that tell a molecular story of health and disease. This year's focus is the structural view of sugar metabolism and its complications leading to diabetes. To get started, teams are encouraged to use PDB-101 materials related to diabetes and molecular visualization.

Videos may be submitted from March 8 - May 29, 2016 for review by our esteemed panel of judges. Award winners will be announced on June 14, 2016.



Paper Published in Journal of Applied Crystallography

03-May-2016

DCC: a Swiss army knife for structure factor analysis and validation
H. Yang, E. Peisach, J. D. Westbrook, J. Young, H. M. Berman and S. K. Burley
J. Appl. Cryst. (2016). 49 doi: 10.1107/S1600576716004428

DCC is a wrapper for third-party software packages to aid in structure factor analysis and validation. As the results are recorded in PDBx/mmCIF format, the output from DCC can be used in automatic data pipelines.

The program can be downloaded from sw-tools.rcsb.org.

A full list of RCSB PDB publications is available.



New Insulin and Diabetes Poster Available for Download

26-Apr-2016

The new Insulin and Diabetes poster illustrates how structural biology has revealed the details of insulin signaling and how this knowledge is being used to create new and better treatments for diabetes

The poster is built around the watercolor painting Insulin in Action, which includes glucose (small white circles), insulin (yellow), and the insulin receptor (light green), among others.

Explore more resources and articles about insulin and diabetes using the PDB-101 Browser.


Insulin in Action


DNA Day 2016: April 25

19-Apr-2016

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


Spring Newsletter Published

12-Apr-2016

The Spring 2016 issue of the RCSB PDB Newsletter is now available.

Articles highlight Wellcome Trust Image Awards, visualization of electron density maps for ligands, the 2016 High School Video Challenge, and more.



This issue's Education Corner is related to the Video Challenge. In this interview, Jed Dannenbaum, a USC Professor of the Practice of Cinematic Arts, gives advice on telling scientific stories with videos.

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



Molecular Origami: 3D model of Zika virus

05-Apr-2016

Last week, the 3D structure of the Zika virus, determined by cryo-electron microscopy, was released in the PDB archive. Public availability of the Zika virus atomic coordinates to medical researchers worldwide will accelerate new antiviral drug and vaccine development.

PDB ID: 5ire

The 3.8Å Resolution Cryo-EM Structure of Zika Virus
Devika Sirohi, Zhenguo Chen, Lei Sun, Thomas Klose, Theodore C. Pierson, Michael G. Rossmann, Richard J. Kuhn
Science (2016) doi: 10.1126/science.aaf5316


Build a paper model of the Zika virus based on this entry in this new PDB-101 activity.



Paper Published in Journal of Chemical Education

29-Mar-2016

Read about RCSB PDB resources and how they can be used in research and education:

RCSB Protein Data Bank: A Resource for Chemical, Biochemical, and Structural Explorations of Large and Small Biomolecules
(2016) Christine Zardecki, Shuchismita Dutta, David S. Goodsell, Maria Voigt, and Stephen K. Burley
J. Chem. Educ., 2016, 93 (3), pp 569-575 doi: 10.1021/acs.jchemed.5b00404

A full list of RCSB PDB publications is available.



Improving Download Services

22-Mar-2016

Website/HTTP access to PDB data files is improving as RCSB PDB moves to a scalable, cloud-based service that will better support our growing user community. Access to this service via http://files.rcsb.org is not rate-limited or throttled for heavy users, and programmatic usage is encouraged.

This method is being used to deliver PDB entry data files (PDB and PDBx/mmCIF formats) from the Download Tool and from Structure Summary pages (Display and Download options). Data are returned faster and more reliably.

Download files from http://files.rcsb.orgDisplay and download PDB data faster.


Simplified URLs point to compressed and uncompressed files to better enable use of PDB data in software applications:

Action Example URLs
(action/content is in bold)
Directly display PDB entries in PDB or PDBx/mmCIF format in a web browser http://files.rcsb.org/view/1stp.pdb
http://files.rcsb.org/view/1stp.cif
Download data files (uncompressed or compressed) http://files.rcsb.org/download/1stp.pdb
http://files.rcsb.org/download/1stp.cif
http://files.rcsb.org/download/1stp.pdb.gz
http://files.rcsb.org/download/1stp.cif.gz
Access an entry's non-coordinate information (authorship, citation, database references, etc.) http://files.rcsb.org/header/1stp.pdb
http://files.rcsb.org/header/1stp.cif
Improving access to entry data files was the first step in a phased approach; we will continue to improve download services. Comments and questions are welcomed.


RCSB PDB Highlighted at Wellcome Image Awards

15-Mar-2016

Two RCSB PDB images have been highlighted with 2016 Wellcome Image Awards. David S. Goodsell's painting of Ebola Virus Proteins has been selected as the overall winner, with Maria Voigt's molecular animation of Clathrin also recognized with an award.

Goodsell's painting was created for his RCSB PDB Molecule of the Month article on Ebola Virus Proteins, and also turned into a related video. This intricate painting shows this tiny, notoriously lethal virus in minute detail, using the structural information available in the Protein Data Bank archive.

Voigt's Clathrin illustration is part of RCSB PDB's traveling Art of Science exhibit, which uses the context of a community art gallery to introduce new audiences to to the beauty of structural biology. This exhibit is currently on display at the FlexSchool in Fanwood, NJ.

These are two of the 20 winning images selected as the best in science image making from all those acquired by the Wellcome Images picture library in the past year. The awards were presented at a ceremony at the Science Museum in London on March 15, where the images are now on show to the public. Other award-winning images include pathways of nerve fiber in the brain, delicate golden scales on a Madagascan sunset moth and a digitally reconstructed skeleton showing atheroma, the "furring up" of arteries that supply blood to the brain which can cause stroke.

16 science centers, museums and galleries will be displaying the winning images in their own styles to spark imaginations everywhere. This year the images will also be appearing as far afield as the Africa Centre for Population Health in South Africa, the Polytechnic Museum in Moscow, Russia, and the Massachusetts Institute of Technology.

The images are available to view on the Wellcome Image Awards website along with the stories behind the images and their creators. The images already feature in Wellcome Images collections, where they can be accessed and used along with more than 40,000 other contemporary biomedical and clinical images. The Awards were established in 1997 to reward contributors to the collection for their outstanding work.


Ebola Virus Proteins, by David S. Goodsell. The virus is surrounded by a membrane (pink/purple) stolen from an infected cell. This is studded with proteins from the virus (turquoise) which extend outwards and look like trees rooted in the membrane. These proteins attach to the cells that the virus infects. A layer of proteins (blue) supports the membrane on the inside. Genetic information (RNA; yellow) is stored in a cylinder (nucleocapsid; green) in the centre of the virus. More at Molecule of the Month on Ebola Virus Proteins.

Clathrin, by Maria Voigt. Clathrin is a protein found in cells which forms basket- or cage-like structures around small membrane sacs. These clathrin cages help bring molecules into the cell and then carry them around inside from one place to another. They also help sort through the molecules (which can include receptors and nutrients) so that different cargo is efficiently delivered to different destinations. Some disease-causing germs and toxins hijack this process and use it to infect cells.  More at Molecule of the Month on Clathrin.


Visualize Electron Density Maps For Bound Ligands

08-Mar-2016

View sigma-weighted 2m|Fo|-d|Fc| electron density "mini-maps" for bound ligands using the JSmol 3D View. This feature is available for ligands with more than one atom (ions excluded) in PDB entries with structure factor data. Different sigma values can be selected.

The feature can be accessed from an entry's Structure Summary page in the Small Molecule's section or from the bottom of the 3D View page.

  • Retinoic Acid in PDB ID 1CBS
    Electron density mini-map for Retinoic Acid in PDB ID 1CBS at sigma level 1. In this example, the ligand fits well into the density.
  • Thymidine-5'-Phosphate in PDB ID 3HW4 at sigma level 2
    Electron density mini-map for Thymidine-5'-Phosphate in PDB ID 3HW4 at sigma level 2. Electron density is only available for part of the ligand.


Electron Density (JSmol) button from the Structure Summary page for PDB entry 1CBS.

Options to view different ligands and mini-maps and to change sigma levels appear under the JSmol viewer for PDB entry 1PRC.


Gene View Video Tutorial

01-Mar-2016

RCSB PDB's Gene View illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB protein chains (chosen from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.



A new video tutorial gives an overview


1 Billion Atoms

23-Feb-2016

PDB is now a billion-atom archive. Over a hundred thousand entries--proteins, DNA, RNA, and all the tiny molecules associated with them--capture the nanoscale details of these billion atoms. Use RCSB PDB's to start exploring:

  • Search features at rcsb.org include simple text searching (with autosuggestions), browsing based on common characteristics (experimental method, organism, taxonomy, etc.), and an option to build complex queries with Advanced Search.
  • Molecular viewers, including JSmol/Jmol, Protein Viewer, and the RCSB PDB's Protein Workshop help users interactively view PDB's atomic structures.
  • Molecule of the Month: Hosted at PDB-101, the educational portal of the RCSB PDB, nearly 200 Molecule of the Month articles describe molecular structure and function with interactive views, discussion topics, and links to structure examples.


1 Billion Atoms


Search Results, Simplified.

16-Feb-2016

Searches at rcsb.org now return PDB structures using a redesigned layout. The user interface puts the structures at the top of the page. The left column provides summary information at a glance by indicating the distribution of structures in categories, including by organism, UniProt molecule name, taxonomy, and more. A search for collagen, for example, shows that 277 structures related to collagen were determined by X-ray crystallography. The items in this column can also be used to refine a search. In this same example, clicking on X-ray Resolution less than 1.5 Å will display the corresponding high resolution structures.

Similar to RCSB PDB's home page and Structure Summary pages, the responsive layout of the Search Results page is designed to appear well on mobile devices.

Search Results can be used to generate tables, download data, and create galleries of images. For more information, view the What's New page or enter a search term in the top box.



2016 High School Video Challenge: Structural Biology and Diabetes

09-Feb-2016

For the third year, RCSB PDB invites all high school students to create short videos that tell a molecular story of health and disease. This year's focus is the structural view of sugar metabolism and its complications leading to diabetes. To get started, teams are encouraged to use PDB-101 materials related to diabetes and molecular visualization.

Videos may be submitted from March 8 - May 29, 2016. Award winners will be announced on June 14, 2016.

For more information, sign up for the Video Challenge Monthly Newsletter or visit the challenge webpage.


Insulin in action: View of insulin (white oval) and and related signaling proteins in the cell.


Many resources are offered to help students get started, including a paper model of insulin.


Protein Modeling at the Science Olympiad

02-Feb-2016

Protein modeling is one of several competitive events taking place 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.

In protein modeling, teams of high school students demonstrate their understanding of protein structure and function by building 3D models. The theme of this year's event, designed by MSOE and RCSB PDB, is focused on biosynthesis and subsequent signaling of dopamine and serotonin.

RCSB PDB recently judged ~100 models in regional competitions in New Jersey, and will also participate in the February San Diego Regional event.

Many thanks to the RCSB PDB judges, 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.



Teams are scored on protein models built in advance, smaller models built during the competition, and a written examTeams are scored on protein models built in advance, smaller models built during the competition, and a written exam.


Molecular Explorations Through Biology and Medicine

26-Jan-2016

The online portal PDB-101 is aimed at teachers, students, and the general public to promote molecular explorations through biology and medicine. 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.

The PDB-101 resource has been reorganized to provide better access to curricular materials, paper models, Molecule of the Month articles, and other materials developed by the 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 immune system and renewable energy.

2016 Calendar Cover
A new calendar highlighting protein-drug complexes in the PDB archive is available for download in PDF (4 MB) and PowerPoint (20 MB) formats from PDB-101.


Winter Newsletter Published

19-Jan-2016

The Winter 2016 issue of the RCSB PDB Newsletter is now available.

Articles highlight 2015 statistics, the new wwPDB Deposition Tool, RCSB PDB's 2016 protein-drug calendar, website features for query and analysis, and more.

In this issue's Education Corner, CCDC's Amy Sarjeant describes Using 815,527 Crystal Structures to Teach Chemistry: The Cambridge Structural Database.

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



Deposit 3DEM, NMR, and X-ray Structures with new Deposition Tool

12-Jan-2016

Since January 2014, the new wwPDB Deposition & Annotation (D&A) system has been used to submit and annotate >12,000 X-ray structure depositions and to release >6,800 entries in the PDB archive.

The wwPDB has now expanded this system to support structures from 3DEM and NMR experiments.  The wwPDB D&A system interoperates with EMDB and BMRB to enable joint depositions of both atomic coordinates (PDB) and electron density maps (EMDB) or NMR experimental data (BMRB). Both PDB and EMDB/BMRB accession codes will be issued simultaneously after the entry is deposited.

Visit wwpdb.org for more information on this new D&A system.



A Year in Protein-Drug Complexes

05-Jan-2016

Year 2016 Calender Cover

A new calendar highlighting protein-drug complexes in the PDB archive is available for download in PDF (4 MB) and PowerPoint (20 MB) formats.

Proteins are tiny molecular machines. While not visible with the naked eye, their structures and functions can be investigated and understood through various experimental methods. Proteins perform many of the tasks needed to support living cells. Illnesses, such as cancer, can occur when they are prevented from performing their normal jobs. Other ailments are caused when foreign proteins (such as from bacteria or viruses) interfere with ours. Most drugs are small chemicals, even smaller than proteins, that work by binding to target proteins and modifying their actions within our cells. Other drugs are modified proteins that can take the place of improperly operating native proteins.

Some of our most powerful anticancer drugs completely disable an essential molecular machine, without which the cell cannot survive. These drugs kill cancer cells outright. Other drugs, such as cholesterol lowering agents, blunt the action of less-critical proteins to benefit patients.

We know a great deal about how drugs work because scientists in academe and the pharmaceutical industry are able to examine drug-protein complexes at the level of individual atoms. These three-dimensional (3D) atomic structures allow us to see how drugs bind to their protein targets in exquisite detail. Frequently, these structures suggest ways to modify the structure of the drug to better fit the target protein, either to improve efficacy or to reduce the likelihood of side effects.  These structures of proteins and drugs highlighted in this calendar, along with many others, can be explored using the RCSB PDB.

A few printed copies are available; please email info@rcsb.org to request a copy.