Training, Outreach, and Education

Viruses

Explore how insights provided by structural biology are used to develop new defenses against viral infection.

Viruses are a major threat to global health. Historically, pandemics of influenza, polio, smallpox and many other viruses have spread through populations numerous times, killing millions of people. Today, with our continually growing understanding of virus structure and biology, we have many tools to fight viral infection. Antiviral drugs block key viral proteins, preventing their replication and spread, and vaccines prime our immune system to make us ready for future exposure to common viruses.

Poliovirus uses a single protein to replicate its RNA genome (left, with RNA template strand in orange and new RNA strand in yellow). SARS-CoV-2 encodes a multipart complex, including a polymerase (turquoise) and helper proteins (darker blue), a helicase (purple), and a proofreading enzyme (green), which together replicate the RNA genome and add a characteristic cap group to the end of some copies to make a messenger RNA.

Health and Nutrition

Explore how insights provided by structural biology increase our understanding of health and nutrition.

Our cells make about 20,000 types of proteins, as well as many types of nucleic acids, carbohydrates, lipids, and small molecules. By understanding the structure and function of these molecules, we can ensure that they are performing at their peak. This includes ensuring that we have sufficient raw materials to build and power all of these molecules, and knowing when we need to step in ourselves and modify the action of these molecules with drugs and other medical interventions. This knowledge informs the ways that we all can live our best lives, at all stages of our lives.

Thirteen vitamins essential to the human diet.

Read how the ModelCIF data framework (details) and RCSB PDB APIs (documentation) each support exploration of Computed Structure Models (CSMs).

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models
B. Vallat, G. Tauriello, S. Bienert, J. Haas, B.M. Webb, A. Žídek, W. Zheng, E. Peisach, D.W. Piehl, I. Anischanka, I. Sillitoe, J. Tolchard, M. Varadi, D. Baker, C. Orengo, Y. Zhang, J.C. Hoch, G. Kurisu, A. Patwardhan, S. Velankar, S.K. Burley, A. Sali, T. Schwede, H.M. Berman, J.D. Westbrook

(2023) Journal of Molecular Biology 435: 168021 doi:10.1016/j.jmb.2023.168021
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances
S. Bittrich, C. Bhikadiya, C. Bi, H. Chao, J.M. Duarte, S. Dutta , M. Fayazi, J. Henry, I. Khokhriakov, R. Lowe, D.W. Piehl, J. Segura, B. Vallat, M. Voigt, J.D. Westbrook, S.K. Burley, Y. Rose
(2023) Journal of Molecular Biology 435: 167994 doi:10.1016/j.jmb.2023.167994

This Fall, RCSB PDB met with undergraduate and graduate students at two important meetings: The SACNAS National Diversity in STEM (NDiSTEM) and the Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS) meeting.
Students were encouraged to learn more about

1. Summer internships for undergraduates in software development
2. Gap Year Opportunities For Scientific Software Developers
3. Postdocs and other open positions
4. Training Events

At ABRCMS, several students who collaborated with the RCSB PDB and the Rutgers Institute for Quantitative Biomedicine presented their work:

1. Rusham Bhatt (UMBC) presented Enabling Computational Biology Research Using Python-Based Applications
2. Gigi Lin (Hunter College) presented A Multidisciplinary Approach Towards Elucidating the Molecular Sociology of Fungal Plasma Membrane Proteins
3. Isabel M. Meléndez (University of Puerto Rico at Mayagüez) Computational Studies of the 8-17 DNAzyme in solution with the presence of Mg^2+

Isabel’s work was recognized for outstanding presentation in the category of Computational and Systems Biology at ABRCMS.

Rusham Bhatt; Gigi Lin (right) with her mentor Jennifer Jiang; and Isabel Meléndez at ABRCMS

Snapshots from the life cycle of bacteriophage T4. At left, a bacteriophage (red) is injecting its DNA genome (white) into an Escherichia coli cell. At center, the bacteriophage has taken over the cell, destroying the cellular DNA (purple) and forcing the cell to make many new copies of itself. At right, the bacteriophage produces a channel-forming protein (magenta) that pierces the inner cell membrane, allowing lysozyme enzymes to break down the peptidoglycan sheath (fibrous molecules shown in turquoise between the two cellular membranes) that supports the cell. The cell bursts, releasing several hundred new bacteriophages.

Many structures of parts of bacteriophage T4 are available in the PDB archive, including the head that holds the DNA in PDB ID 7vs5 (mature form) and 7vrt (immature form), and the baseplate with the injection machinery in PDB ID 5iv5.

This painting is part of PDB-101's SciArt gallery of Molecular Landscapes by David S. Goodsell.

Image Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank and Scripps Research. doi: 10.2210/rcsb_pdb/goodsell-gallery-048

The wwPDB Foundation made awards to outstanding student posters at the 2023 Annual Symposium of The Protein Society (July 13-16, Boston, MA).

Taylor M. Laflamme for
Specificity studies of small molecule inhibitors targeting the ankyrin repeat oncoprotein gankyrin
Taylor M. Laflamme (1), Emma I. Kane (1), Dipti Kanabar (2), Tejashri Chavan (2), Aaron Muth (2), & Donald E. Spratt (1)

1) Clark University; 2) St. John's University

Kevin Ramirez for
Host protein decoy fluorescence sensors for the detection of SARS-CoV-2 virions
Kevin Ramirez (1,2), David Bouzada (3), Arjan Bains (1,2), Mourad Sadqi (1,2), Eugenio Sentís-Vazquez(3), Patricia LiWang (1,2), and Victor Muñoz (1,2)

1) Department of Bioengineering, 2) CREST Center for Cellular & Biomolecular Machines, University of California Merced, 3) Universidad de Santiago de Compostela, Spain

Many thanks to The Protein Society organizers and poster prize judges for making these awards possible.

Taylor M. Laflamme and Kevin Ramirez

The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB50 events, workshops, and educational publications. The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.

The wwPDB Foundation is grateful for our industrial sponsors: Discngine, OpenEye Scientific, Roivant Sciences, Rigaku, and ThermoFisher Scientific. Individual sponsorships are also available.

Consider supporting the next 50 years of PDB's spirit of openness, cooperation, and education with a donation to the wwPDB Foundation.

Visit PDB-101 to learn the basics of RCSB PDB APIs. Learn from the RCSB PDB software developers how publicly available APIs build on the data available in the PDB archive and additional internal and external annotations.

Watch recordings of the Leveraging RCSB PDB APIs for Bioinformatics Analyses and Machine Learning

These videos will be of interest to researchers in bioinformatics or structural biology; researchers who need to cross- reference PDB and data from other resources; and anyone interested in large scale analyses of structural data (experimental or computational).
Topics include:

1. Introduction to RCSB PDB APIs and Data Schema
2. RCSB PDB Data API
3. RCSB PDB Search API
4. Search and Data API Hands-on Teaser
5. Coding Example: Accessing RCSB PDB APIs via Python
6. Coding Example: Preparing a dataset for ML/AI-based prediction of heterodimer binding sites

PDB-101 hosts different Training Events and a specialized Guide to Understanding PDB Data.