News 2019
Happy Birthday, Irving Geis
10/18/2019
From the Bench to Molecule of the Month
10/15/2019
Fall Newsletter Published
10/08/2019
Structural Biology Pipeline Meets the Classroom: First Structure Released
09/25/2019
Illustrate PDB Structures
09/17/2019
Contact Customer Services with Questions and Feedback
09/10/2019
Head Back to School with PDB-101
09/03/2019
Poster Prize Awarded at ISMB
08/27/2019
Poster Prize Awarded at ACA
08/20/2019
Join Our Biocuration Team
08/06/2019
Education Corner: How Does Life Work?
07/23/2019
Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format
07/16/2019
Summer Newsletter Published
07/09/2019
Create a Hemoglobin Bean Bag Toss
07/02/2019
Learn About HIV and AIDS at PDB-101
06/25/2019
New Flyer: Antibiotics in Action
06/04/2019
Annual Report Published
05/21/2019
Award-Winning Videos on Antibiotic Resistance
05/14/2019
Education Corner: Exploring the Molecules of Biological Warfare in Virtual Reality
05/07/2019
Vote Now for the Viewer's Choice Award
04/30/2019
Celebrate DNA Day on April 25
04/23/2019
Spring Newsletter Published
04/16/2019
Take the Molecule of the Month User Survey and Enter to Win
04/09/2019
High School Students: Submit Antibiotic Resistance Videos Before April 23
04/02/2019
Molecular Landscapes and the Art of Science
03/26/2019
The PDB Archive Reaches a Significant Milestone
03/19/2019
New Video: Penicillin and Antibiotic Resistance
03/05/2019
Superbugs! How Bacteria Evolve Resistance to Antibiotics
02/26/2019
Join Our Team as a Biocurator
02/12/2019
New Online Curriculum: The PDB Pipeline & Data Archiving
02/05/2019
Education Corner: Improving Visual Literacy
01/29/2019
Winter Newsletter Published
01/15/2019
2018 FASEB BioArt Winner
01/08/2019
2019: What is a protein?
01/01/2019

Happy Birthday, Irving Geis

10/18/2019

RCSB PDB News ImageMyoglobin Fold (1987). Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.
RCSB PDB News ImagePhoto by Sandy Geis

Irving Geis (October 18, 1908-July 22, 1997) was a gifted artist who helped illuminate the field of structural biology with his iconic images of DNA, hemoglobin, and other important macromolecules. To celebrate Irving Geis' birthday, we invite you to tour the Geis Digital Archive.

Through a collaboration with the Howard Hughes Medical Institute (HHMI), which owns the Geis Archives, RCSB PDB has established a digital archive of Geis' molecular art. This resource displays many of Geis' illustrations in the context of the corresponding PDB structures and related molecular information. These images are also made available for download for noncommercial usage.

Under the direction of RCSB PDB team members, the Geis Digital Archive is being developed by undergraduates. Students created modern visualizations of the molecules featured in Geis' work, and researched the structures to provide background and supporting information about the illustrations. Alex Alvarado (University of Southern California) and Nicole Werpachowski (Fordham College at Lincoln Center) created the initial design of the resource as part of their Rutgers RiSE (Research in Science and Engineering) experience. Their work was funded during the summer of 2015 by an NSF REU. Rutgers students Belle Lin (2015-2016) and Christopher Markosian (2015-2016) continued work on the project. In 2016, Raheel Ahmad (Rutgers), Pamela Amechi (University of Maryland Baltimore Country), and Keyerra Daniels (Winthrop University) expanded the archive as part of the Rutgers RiSE program.

Thanks to the Howard Hughes Medical Institute for their work on this project. Questions about the HHMI Geis Archives should be sent to archives@hhmi.org.

RCSB PDB News ImageImage of Lysozyme by Irving Geis. Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.
RCSB PDB News ImageImage of PDB ID 1LYZ can be launched in 3D using Jmol.
RCSB PDB News ImageAlex Alvarado, Sandy Geis (Irving's daughter), and Nicole Werpachowski
RCSB PDB News ImageBelle Lin and Christopher Markosian
RCSB PDB News ImageKeyerra Daniels, Raheel Ahmad, and Pamela Amechi


From the Bench to Molecule of the Month

10/15/2019

Galyna Khramova (University of Florida) spent most of her summer at Rutgers thinking about Controlling the activity profile of a multifunctional enzyme: site-directed mutagenesis of mouse DXO in a project split between RCSB PDB and the Kiledjian Lab in the Department of Cell Biology and Neuroscience. Her time spent with the RCSB PDB team also led to a collaboration with David Goodsell on this month’s Molecule of the Month.

The series presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.

In addition to this column, Galyna also created JSMol views for Molecule of the Month features on amylase, pepsin, and potassium channels.

Galyna was part of the Rutgers University RISE (Research in Science and Engineering) program. RISE at Rutgers is a nationally acclaimed summer research program for outstanding undergraduates from diverse backgrounds. Scholars participate in 10 weeks of cutting-edge research in the biological, physical, and social/ behavioral sciences, math, engineering, and exciting interdisciplinary areas under the guidance of carefully matched faculty mentors. A comprehensive professional development component complements the research.

RCSB PDB News ImageBiocurator Luigi Di Costanzo, RISE Scholars Jitendra Singh and Galyna Khramova, and Biocurator Brian Hudson

Interested in interning with the RCSB PDB? RISE applications will open on November 1, 2019. The program particularly encourages applications from students from underrepresented, disadvantaged, non-traditional or first-generation college backgrounds or who attend schools with limited research opportunities.


Fall Newsletter Published

10/08/2019

The Fall 2019 issue of the RCSB PDB Newsletter is now online.

This issue highlights High school students releasing a PDB structure; PDB versioning; Structure Quality Metrics; Illustrating PDB Structures in the Molecule of the Month style; and more.

The Education Corner highlights outreach initiatives are making structural biology fun and accessible for broad audiences while highlighting specific experimental techniques. Deep Learning, Citizen Science & Puppies by Michele Darrow (Diamond Light Source) describes the path towards segmentation of a cryoEM dataset of a virus infected cell, while Fiacre Kabayiza and Bill Bauer (BioXFEL) describe XFEL Crystal Blaster: an educational game.


Structural Biology Pipeline Meets the Classroom: First Structure Released

09/25/2019

Last Fall, the RCSB PDB Newsletter highlighted Structural Biology Pipeline Meets the High School Classroom. For this feature, Biology Teacher Dan Williams coordinated articles from the point of view of students and of teachers from Long Island, NY involved in SPARK (Students Partnerships for Advance Research and Knowledge), a collaborative program by the Office of Educational Programs and NSLS-II at Brookhaven National Laboratory (BNL).

With this week’s update of the PDB, the first structure from this program, a methylenetetrahydrofolate reductase (MTHFR) was made publicly available as PDB entry 6PEY.

Shelter Island students Emma Gallagher and Lauren Gurney worked in collaboration with students from across Long Island to perform hundreds of crystallization reactions, freeze the MTHFR crystals in liquid nitrogen, and obtain X-ray diffraction data using the AMX beamline at Brookhaven National Laboratory’s National Synchrotron Light Source II. Countless hours were spent analyzing the data using standard structural biology programs such as CCP4 and COOT.

MTHFR has been implicated in many human diseases including but not limited to cardiovascular disease and miscarriage. It is hoped that further examination of this structure will help scientists, like these students, understand how MTHFR works and lead to better treatments.

Thanks to the SPARK program, high school students like Emma and Lauren and hundreds of other Long Islanders have joined the worldwide PDB Data Depositors community. Soon, other PDB structures from this program will be released. By working together, all of the students in the SPARK program have helped make each other to be better scientists.

This achievement was made possible by the continuous guidance and support of the scientists in BNL’s SPARK program and Office of Educational Programs, Dr. Aleida Perez, Dr. Alexei Soares, and Dr. Vivian Stojanoff.

For more, see Structural Biology Pipeline Meets the High School Classroom.

RCSB PDB News ImageMural at Shelter Island High School inspired by the SPARK program and the RCSB PDB-ACA Coloring Book.


Illustrate PDB Structures

09/17/2019

Over the years, Molecule of the Month illustrations have become easily recognizable thanks to their non-photorealistic rendering, flat pastel colors, and black outlines.

The new program Illustrate generates these image for use in dissemination, outreach, and education. Use the interactive web interface or download the open-source Fortran code from GitHub.

Illustrate is described in:

David S. Goodsell, Ludovic Autin, and Arthur J. Olson Illustrate: Software for Biomolecular Illustration, Structure (2019) doi: 10.1016/j.str.2019.08.011

RCSB PDB News ImageComplex of tRNA with EF-Tu (PDB structure 1ttt, see Molecule of the Month on Elongation Factors). Image created using Illustrate.


Contact Customer Services with Questions and Feedback

09/10/2019

RCSB PDB's Customer Services collects and answers questions about the website, PDB data, and structural biology. Nearly 1000 unique users initiate new electronic conversations 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, Website FAQ, Guide to Understanding PDB Data, and a Service Status page that indicates if all online services are up and running.

An orange Contact Us button appears on every RCSB.org page. Let us know what you think--we love to hear from you.

RCSB PDB News Image
RCSB PDB News Image


Head Back to School with PDB-101

09/03/2019

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.


Poster Prize Awarded at ISMB

08/27/2019

At this year's meeting of the Intelligent Systems for Molecular Biology Conference (ISMB)/European Conference on Computational Biology, the award went to João Rodrigues for pdb-tools: a dependency-free cross-platform swiss army knife for PDB files for Learning from the ligand: improving binding affinity prediction using molecular descriptors.

pdb-tools: a dependency-free cross-platform swiss army knife for PDB files for Learning from the ligand: improving binding affinity prediction using molecular descriptors. João Rodrigues (Stanford University), João Teixeira (University of Toronto), Mikael Trellet (Utrecht University), and Alexandre Bonvin (Utrecht University)

The pdb-tools are a collection of Python scripts for working with molecular structure data in the Protein Data Bank (PDB) format. The tools allow users to easily and efficiently edit and validate PDB files as well as convert coordinate data to and from the now-standard mmCIF format. Moreover, their simple and consistent command-line interface makes them particularly adequate for non-expert users. All tools are implemented in Python, without external dependencies, and are freely available under the open-source Apache License at https://github.com/haddocking/pdb-tools and on PyPI.

Many thanks to Chair Arjun Krishnan (Michigan State University), Co-Chairs Casey Greene (University of Pennsylvania) and Virginie Uhlmann (EMBL-EBI), and Steven Leard (ISMB).

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

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Poster Prize Awarded at ACA

08/20/2019

At this year's American Crystallographic Association's Annual Meeting, the RCSB PDB Poster Prize award went to Shaobo Dai for Structural basis of SETD3 as an actin histidine methyltransferase SETD3

Shaobo Dai, John R. Horton, Clayton B. Woodcock (The University of Texas MD Anderson Cancer Center), Alex W. Wilkinson (Stanford University), Xian Zhang, Or Gozani, Xiaodong Cheng (The University of Texas MD Anderson Cancer Center)

Many thanks to Poster Prize Chairs Louise Dawe (Wilfrid Laurier University) and David R. Rose (University of Waterloo) and the judges.

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

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Join Our Biocuration Team

08/06/2019

RCSB PDB is looking for a Biochemical Information & Annotation Specialist to join the RCSB PDB team at Rutgers, The State University of New Jersey.

The Challenge: Curate, validate, and standardize macromolecular structures from the PDB community. Participate in exciting projects with significant impact on the scientific community. 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 Image
RCSB PDB News ImageRCSB PDB Team from Rutgers


Education Corner: How Does Life Work?

07/23/2019

The Summer 2019 issue of the RCSB PDB Newsletter is now online.

In the Education Corner, Joel Kowit describes his artistic approach in How Does Life Work? Creating Scientific Explanations in Stained Glass.

Other newsletter articles in this issue include the Impact of PDB Structures on US FDA Drug Approvals; OneDep Improvements: Ligand Validation Images and Electron Density Maps; Award-winning videos; and more.

RCSB PDB News ImageHis exhibition The Cellular Universe Through Stained Glass will be on display July 3 through September 9 at the NRB/New Research Building at Harvard Medical School. An Opening Reception and Talk will take place July 24, 4-6 pm, 2019.


Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format

07/16/2019

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.

What does PDBx mean? Where are all the hydrogen atoms in this file? Should I care about the R-factor? Why are there 20 overlapped structures in my file? These questions and many others are explored in PDB-101's Guide to Understanding PDB Data. This resource 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.

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A Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format has been added to this collection. The PDBx/mmCIF file format and data dictionary is the basis of wwPDB data deposition, annotation, and archiving of PDB data from all supported experimental methods. And as of July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory.

This guide highlights the Basics of Syntax and Format, provides Format Examples, and describes Entities, Parent-child Relationships, and the Chemical Component Dictionary.


Summer Newsletter Published

07/09/2019

The Summer 2019 issue of the RCSB PDB Newsletter is now online.

This issue highlights the Impact of PDB Structures on US FDA Drug Approvals; OneDep Improvements: Ligand Validation Images and Electron Density Maps; Award-winning videos; and more.

In the Education Corner, Joel Kowit describes How Does Life Work? Creating Scientific Explanations in Stained Glass.


Create a Hemoglobin Bean Bag Toss

07/02/2019

In 1962, Max Ferdinand Perutz and John Cowdery Kendrew received the Nobel Prize in Chemistry "for their studies of the structures of globular proteins."

HemoHole is a game where hemoglobin has holes where the heme bean-bags can be tossed through. It was created at Rutgers by Institute for Quantitative Biomedicine graduate students Kristin Blacklock, Elliott Dolan, Will Hansen, Nancy Hernandez, and Dmitri Zorine.

Visit PDB-101 to download the SVG files used to create HemoHole and to learn more about hemoglobin, myoglobin, PDB Pioneers, and Structural Biology and Nobel Prizes.

RCSB PDB News ImageThe hemoglobin image was broken into two SVG files and laser cut/etched.
RCSB PDB News ImageHemoHole is a game where hemoglobin has holes where the heme bean-bags can be tossed through.


Learn About HIV and AIDS at PDB-101

06/25/2019

The AIDS epidemic began a few decades ago and since then scientists have revealed the atomic structures of most of the molecules in HIV. Using these structures, researchers have designed new treatments for HIV infection, which are now part of effective drug regimens that halt the growth of the virus. Structures of HIV molecules also provide new hope for development of vaccines and methods to rid an infected individual of the latent virus.

PDB-101 hosts a variety of related educational materials, including Molecule of the Month features, a paper model of the HIV capsid, videos, and more.

RCSB PDB News ImageHIV in Blood Plasma, 1999 by David S. Goodsell, The Scripps Research Institute. Available at PDB-101 as part of the David Goodsell SciArt Gallery.


New Flyer: Antibiotics in Action

06/04/2019

Antibiotics allow us` to fight infections by pathogenic bacteria. They attack essential molecular machines in bacteria, stopping or slowing their action, ultimately slowing growth or killing the cell.

Download a new flyer that illustrates some classes of antibiotics and their target protein/molecule organized by the biochemical pathway they interrupt.


Annual Report Published

05/21/2019

Download the 2018 Annual Report (PDF) for an overview of recent Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education activities.

This review highlights many RCSB PDB accomplishments, including a look at the global impact of the resource.

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

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Award-Winning Videos on Antibiotic Resistance

05/14/2019

The sixth edition of the Video Challenge for High School Students shows how high school students are excellent science communicators. Submitted videos demonstrate tremendous creativity, and used many storytelling approaches to communicate the Mechanisms of Bacterial Resistance to Aminoglycoside Antibiotics.

Our panel of expert judges (Disan Davis (RockEDU Science Outreach, The Rockefeller University), Ella Marushchenko (Ella Maru Studio, Inc.), and Andrew G. McArthur (McMaster University, and the Comprehensive Antibiotic Resistance Database (CARD)) scored the videos based on Quality of Storytelling (20%), Quality of Science Communication (30%), Quality of Public Health Message (10%), Originality and Creativity (20%), Quality of Production (10%), and Proper Accreditation (10%).

The general public voted for the Viewer's Choice Award.

Congratulations to the 2019 Prize Winners

  • First Place: The Criminal Case of the Aminoglycoside Misuser by Brean Bognot and Cayla Tolentino of Mira Mesa High School, San Diego, CA (Team Advisor: Lisa Yoneda)
  • Second Place: New Arms Race Aminoglycoside Antibiotics by Anvi Surapaneni and Vivian Hir of The Quarry Lane School, Dublin, CA (Team Advisor: Alina Hamm)
  • Third Place: The Three Little Bacteria and the Big Bad Tobramycin by Carlos Hernandez, Jeff Huang, and Shamir Sheikh of Stuyvesant High School, New York, NY (Team Advisor: Gilbert Papagayo)
  • Viewer's Choice: Mechanisms of Aminoglycoside Antibiotic Resistance by Charumathi Badrinath of Rye Country Day School, Rye, NY (Team Advisor: Jennifer Doran)

All submitted videos can be seen online.

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

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Education Corner: Exploring the Molecules of Biological Warfare in Virtual Reality

05/07/2019

The Spring 2019 issue of the RCSB PDB Newsletter is now online.

In the Education Corner, Steve McCloskey (Nanome Inc.) describes Exploring the Molecules of Biological Warfare in Virtual Reality.

Other newsletter articles in this issue include a Milestone 150,000 Structures; Superbugs! How Bacteria Evolve Resistance to Antibiotics; a Molecule of the Month User Survey; and more.


Vote Now for the Viewer's Choice Award

04/30/2019

RCSB PDB challenged high school students to create short videos that tell stories about bacterial resistance to aminoglycoside antibiotics.

Watch the challenge entries online and cast your vote for your favorite video before May 7.

Award winners will be announced on rcsb.org and pdb101.rcsb.org on May 14, 2019.


Celebrate DNA Day on April 25

04/23/2019

DNA Day commemorates the completion of the Human Genome Project in 2003 and the discovery of DNA's double helix in 1953. Celebrate by:

RCSB PDB News ImageDNA and RNA are the cell’s way of storing and deploying genetic information. Structural biology is revealing that some nucleic acids also fold to form complex molecular machines. Guided by these structures, nanotech scientists are building new machines composed of nucleic acid. Learn more at PDB-101


Spring Newsletter Published

04/16/2019

The Spring 2019 issue of the RCSB PDB Newsletter is now online.

This issue highlights a Milestone 150,000 Structures; Superbugs! How Bacteria Evolve Resistance to Antibiotics; a Molecule of the Month User Survey; and more.

In the Education Corner, Steve McCloskey (Nanome Inc.) describes Exploring the Molecules of Biological Warfare in Virtual Reality.


Take the Molecule of the Month User Survey and Enter to Win

04/09/2019

RCSB PDB wants to learn more about Molecule of the Month readers worldwide.

Please take this brief survey and be entered into a drawing for a signed copy of The Machinery of Life.


High School Students: Submit Antibiotic Resistance Videos Before April 23

04/02/2019

Antibiotic resistance is one of today's growing problems. Help increase awareness by participating in the 2019 Video Challenge for High School Students on Mechanisms of Bacterial Resistance to Aminoglycoside Antibiotics.

Submit your entry on or before April 23, 2019. Visit PDB-101 for contest details, resources, guidelines, and the panel of expert judges.

RCSB PDB News Image


Molecular Landscapes and the Art of Science

03/26/2019

RCSB PDB News Image

Brain – wider than the sky exhibits artwork about the about the brain for all ages at the Calouste Gulbenkian Museum in Lisbon. Available until June 10th, Brain – wider than the sky features video installations on the brain, interactive sensory exhibits, artworks and digital games to showcase the themes of the exhibition.

New watercolor paintings Excitatory and Inhibitory Synapses by Molecule of the Month creator David Goodsell are on display. Can't make the exhibit? Visit PDB-101 for a new digital gallery of Goodsell's SciArt work.

RCSB PDB News ImageMeasles Virus Proteins (2019)

Goodsell's molecular landscapes are now available from PDB-101 in a special SciArt Digital Archive. These watercolor paintings integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. These illustrations are free for use under CC-BY-4.0 license. Acknowledgement should be given as indicated for each illustration.

RCSB PDB News ImageMyoglobin Fold (1987). Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.

The Goodsell Gallery accompanies PDB-101's Irving Geis Digital Archive. Geis (1908-1997) was a gifted artist who helped illuminate the field of structural biology with his iconic images of DNA, hemoglobin, and other important macromolecules. Through a collaboration with the Howard Hughes Medical Institute (HHMI), which owns the Geis Archives, PDB-101 displays many of Geis' illustrations in the context of the corresponding PDB structures and related molecular information. Through this archive, these images are available for download for noncommercial usage.


The PDB Archive Reaches a Significant Milestone

03/19/2019

With this week's update, the PDB archive has passed the milestone of 150,000 entries, and now contains a total of 150,145.

Established in 1971, this central, public archive has reached this milestone thanks to the efforts of structural biologists throughout the world who collectively contribute a wealth of experimentally-determined protein and nucleic acid structure data, which is made available to researchers all around the world, across many different disciplines.

Four wwPDB data centers support online access to three-dimensional structures of biological macromolecules that help researchers understand many facets of biomedicine, agriculture, and ecology, from protein synthesis to health and disease to biological energy. The archive is large, containing more than 1.9 million files related to these PDB entries and requiring more than 512 gigabytes of storage.

The archive reached the landmark of 100,000 entries in 2014, the International Year of Crystallography. Since that record was set, the PDB continued to grow rapidly, both in number of deposited structures and in the complexity of the data. This growth has been supported by the launch of OneDep, a common global system for deposition, validation, and biocuration of PDB data for supported experimental methods. The OneDep system and the underlying PDBx/mmCIF archive format enable the PDB archive to adapt over time to meet the challenges posed by developments in structural biology. More than 41,000 structures that have been deposited, annotated, and validated using OneDep have now been released into the PDB archive, with many more entries updated to ensure consistency of the archive.

With this week's regular update, the PDB welcomes 262 new structures into the archive. These structures join others vital to research and education in fundamental biology, biomedicine, and bioenergy. Since its inception, the size of the archive has increased tenfold roughly every 10-15 years: the PDB reached 100 released entries in 1982, 1000 entries in 1993, and 10,000 in the year 2000. Now that the 150,000th is made available, more than half of the archive has been released in the past ten years.

The scientific community eagerly awaits the next 150,000 structures and the invaluable knowledge these new data will bring. However, the increasing number, size and complexity of biological data being deposited in the PDB and the emergence of hybrid structure determination methods constitute major challenges for the management and representation of structural data. wwPDB will continue to work with the community to meet these challenges and ensure that the archive maintains the highest possible standards of quality, integrity, and consistency.

Development and future of the PDB archive and wwPDB organization is described in the new reference publication for the PDB archive: Protein Data Bank: the single global archive for 3D macromolecular structure data (Nucleic Acids Res., 2019) and many other papers, including Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (Methods in Molecular Biology, 2017), How community has shaped the Protein Data Bank (Structure, 2013), and Creating a Community Resource for Protein Science (Protein Science, 2012). A full list is available.

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New Video: Penicillin and Antibiotic Resistance

03/05/2019

RCSB PDB News Image

Since its discovery in 1928, penicillin and penicillin-related antibiotics helped save countless lives from bacterial infections. However, in the face of overuse and misuse of antibiotics, bacteria evolved resistance mechanisms that allow them to proliferate even in the presence of the newest antibiotics.

Watch this video to learn how penicillin and penicillin-related antibiotics disrupt the bacterial life cycle, and what molecular mechanisms bacteria employ to evade the action of these drugs.


Superbugs! How Bacteria Evolve Resistance to Antibiotics

02/26/2019

Antibiotics are one of the miracles of modern medicine, allowing us to fight infection by pathogenic bacteria. Antibiotics attack essential molecular machines in bacteria, stopping or slowing their action and ultimately killing the cell.

Superbugs such as MRSA (Methicillin-resistant Staphylococcus Aureus), have found ways to evade almost all current antibiotics.

Download the poster or use the new interactive animation to explore the protein structures that medical researchers are utilizing to search for ways to fight these superbugs.

RCSB PDB News Image
RCSB PDB News Image

PDB-101 offers many other materials focused on Antimicrobial Resistance.


Join Our Team as a Biocurator

02/12/2019

RCSB PDB is looking for a Biochemical Information & Annotation Specialist to join the RCSB PDB team at Rutgers, The State University of New Jersey.

The Challenge: Curate, validate, and standardize macromolecular structures from the PDB community. Participate in exciting projects with significant impact on the scientific community. 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.

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RCSB PDB News ImageRCSB PDB Team from Rutgers


New Online Curriculum: The PDB Pipeline & Data Archiving

02/05/2019

Drawing from their collective knowledge as structural biologists, data scientists, educators, developers and managers of data resources, the Research Collaboratory for Structural Bioinformatics (RCSB) team has created an open access, modular educational curriculum covering concepts, approaches and requirements for developing and managing the data pipeline for a curated public archive of biological experimental data. The online curriculum, available as part of the RCSB PDB-101 education website and also accessible directly via edsb.rcsb.org, makes best practices recommendations for data resource development and management. The intended audience includes scientists, who can use the materials for self-instruction, as well as librarians and information specialists, who can use the materials to develop training services for students, scientists, and staff. In addition, the curriculum is intended to help accelerate development of new data archives for experimental methods used in Integrative Structural Biology. The curriculum is composed of eight modules that can be studied separately or as a complete online course. Materials include professionally produced videos, powerpoint slides, and exercises that guide students step-by-step to design, create, and query their own data archive. This education development project was funded by National Institutes of Health National Library of Medicine as part of the NIH Big Data to Knowledge (BD2K) Initiative (R25 LM012286).

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Education Corner: Improving Visual Literacy

01/29/2019

The Winter 2019 issue of the RCSB PDB Newsletter is now online.

In the Education Corner, Kristen Procko and the BioMolViz Group describe their efforts in Creating Accessible Tools for Molecular Visualization Instruction that are the result of workshops held with broader community of biochemistry, chemistry, and molecular biology educators.

Other newsletter articles in this issue include 2018 milestones and publications, improved support for XFEL/SFX structures, new PDB-101 resources for exploring Molecular Evolution and Antimicrobial Resistance, and more.


Winter Newsletter Published

01/15/2019

The Winter 2019 issue of the RCSB PDB Newsletter is now online.

This issue reviews 2018 milestones and publications, improved support for XFEL/SFX structures, new PDB-101 resources for exploring Molecular Evolution and Antimicrobial Resistance, and more.

In the Education Corner, Kristen Procko and the BioMolViz Group describe Creating Accessible Tools for Molecular Visualization Instruction.


2018 FASEB BioArt Winner

01/08/2019

RCSB PDB News Image

PDB-101's video animation of the calcium pump moving ions across a cell membrane was among the 2018 Winners of FASEB's BioArt Competition. This year’s 10 winning images and three videos represent a wide range of biomedical research, from a Human Hand Showing Carpal Tunnel Tendons and Palm Muscles to a Video of Arabidopsis flowers forming at tip of stem.

The Calcium Pump animation is an excerpt from the introductory What is a Protein? video (also the subject of the 2019 calendar). PDB-101 hosts a collection of videos and animations on a variety of topics.


2019: What is a protein?

01/01/2019

RCSB PDB News Image

Proteins play vital roles in all living organisms. Their specific amino acid sequences give proteins their distinct shapes and chemical characteristics. Proteins rely on the recognition of specific 3D molecular shapes to function correctly for DEFENSE, TRANSPORT, ENZYMES, STRUCTURE, STORAGE, and COMMUNICATION.

These protein shapes and functions are highlighted in this 2019 calendar and other PDB-101 resources.

Download the 2019 calendar (PDF and PPT), the corresponding flyer, and watch the animated video to answer the question What is a protein?


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