Outreach and Education PDB-101 logo

High school students are excellent science communicators. The submitted entries in this year's Video Challenge demonstrate tremendous creativity and used many storytelling approaches to communicate the Molecular Mechanisms of Targeted Cancer Therapies.

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

Congratulations to the 2023 Prize Winners

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Judges' Award First Place and Viewer's Choice Award
Breast Cancer Chess Championship: Trastuzumab vs HER2 Receptor
By Joan Ashreya Mare, Grace Lee, and Ananya Vakkalanka of West Windsor-Plainsboro High School South, West Windsor, New Jersey
Team advisor: Mrs. Meenakshi Bhattacharya

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Judges' Award Second Place
Fighting Cancer by Targetting G12C
By Amanda Nguyen, Kristen Ngo, and Gavin Gonzales of Mira Mesa High School, San Diego, CA
Team advisor: Mrs. Lisa Yoneda

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Judges' Award Third Place
Investigating the Role of VEGF in Targeted Therapy for Cancer
By Victoria Silva of Jericho High School, Jericho, NY
Team advisor: Mrs. Samantha Sforza

Our panel of expert judges (Irina Bezsonova, UCONN Health; Paul Craig, RIT; X.F. Steven Zheng, Rutgers Cancer Institute of New Jersey) scored the videos based on Quality of Storytelling (30%), Quality of Science Communication (30%), Originality and Creativity (20%), Quality of Production (10%), and Proper Accreditation (10%).

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

This marks the 10th and final Video Challenge hosted by PDB-101. Since the inaugural event in 2014, 376 videos have been created by more than one thousand high school students to highlight the structural stories of HIV, Diabetes, Anti-microbial Resistance, Opioids, and Cancer. We thank the teachers and students for their support over the years.

Nucleic Acid Knowledgebase logo

Explore the Structural Biology of Bioenergy Resource to learn how light is absorbed by different organisms. Shown here is the photoactive yellow protein.

A new PDB-101 feature explores how cells capture and utilize many forms of energy to power their molecular processes

Cells expend much of their effort manipulating the environment around them to their advantage. Doing so takes a lot of energy, for example, to power finding food sources, eating and digesting food molecules, and using these molecules to build new cells. For this reason, cells are masters at harnessing diverse sources of energy and putting them to use. Structural biologists are exploring biomolecules that capture and convert energy in cellular processes. New, advanced techniques are being used to reveal the structure and function of these molecules: continued improvement in the resolution of cryoelectron microscopy is revealing complex and larger protein assemblies involved in bioenergy, and split-second serial crystallography with X-ray free electron lasers is giving a close-up look at rapid energetic transitions. PDB structures provide insight into the mechanisms and technology of bioenergy. Visit PDB-101 for more.

The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world and the evolving technologies that can be used to harness the power of these data.

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 or computer science.

Guide topics cover biological assemblies, molecular graphics programs, R-value and R-free, and more. Articles are released to help explain new features as they are added to RCSB.org, such as the inclusion of ofComputed Structure Models at RCSB.org

A new chapter provides an Introduction to RCSB PDB APIs. RCSB PDB APIs build on the data available in the PDB archive and additional internal and external annotations. They power the RCSB.org website. Because they are publicly available, they can be also used without restrictions by users and external resources.

Topics in this article include:

  1. Why APIs?
  2. Accessing Data API through REST services and GraphiQL
  3. Website Access to the API

More detailed user guide documentation is available with links to specific API tutorials and references for more advanced users and developers. Stay up-to-date with API developments by viewing (or subscribing) to the RCSB PDB API announcements Google group.

Visit PDB-101 for more.

A schematic diagram showing the data flow in RCSB's API

RCSB PDB APIs build on the data available in the PDB archive and additional internal and external annotations. They power the RCSB.org website. Because they are publicly available, they can be also used without restrictions by external resources.

Visit PDB-101 to learn the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined 3D biostructures in the PDB. Learn from the RCSB PDB Biocuration Team about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data.
These videos` will be of interest to professionals and graduate students (structural biology, cheminformatics & computational chemistry, bioinformatics & computational biology) interested in learning about strategies to take full advantage of PDB data.

Topics include:

  1. Introduction and course objectives
  2. PDBx/mmCIF format - Not your parents’ legacy PDB format
  3. PDBx/mmCIF data files - Lifting the lid off the black box
  4. Programmatic data access and analysis using PDBx/mmCIF files<

Development and management of the PDBx/mmCIF data dictionary is a collaborative effort involving RCSB PDB, Worldwide Protein Data Bank (wwPDB) partners, and members of the wwPDB PDBx/mmCIF Working Group.

Nucleic Acid Knowledgebase logo

NAKB replaces the Nucleic Acid Database (NDB) resource that will be retired in July 2023.

The Nucleic Acid Knowledgebase (nakb.org) is a new web-based data resource for experimentally-determined structures containing DNA and RNA nucleic acid polymers and their biological assemblies.

NAKB currently indexes 16,000 nucleic acid-containing structures derived from all major structure determination methods (X-ray, NMR, and cryo-electron microscopy), including all held by the Protein Data Bank (PDB), and 48 structures held only by the Nucleic Acid Database (NDB). The resource is updated weekly on Thursdays at noon, US Eastern time.

As the planned successor to NDB (see Developing Community Resources for Nucleic Acid Structures (2022) Life12: 540), NAKB preserves all of the functionality of the legacy service, including search, tabular reports, statistics, 2D and 3D visualization tools, education and standards pages, and a nucleic-acid community web and software resource list.

For each structure, core descriptive information gathered from PDB or NDB is integrated with annotations curated by NDB/NAKB and nucleic-acid centered external resources including RNACentral, Rfam, DNATCO, 3DFootprint, DNAproDB, and BGSU RNA equivalence classes. NAKB also provides interactive tables of nucleotide, base-pair, and base-pair step parameters (DSSR), 2D folding diagrams (RNAView, R2DT), and a 3D viewer (Mol*).

The legacy NDB website (ndbserver.rutgers.edu) will be retired in early 2023. At that time, all NDB web traffic will forward to nakb.org. All links to individual entry NDB atlas pages will automatically redirect to NAKB atlas pages.

NAKB development is funded by National Institutes of Health R01GM085328. NDB has been funded in the past by the National Science Foundation and the Department of Energy.