News 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

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.

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Molecular Landscapes and the Art of Science

03/26/2019

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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

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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.

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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

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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

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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.