Training, Outreach, and Education

RCSB PDB will soon announce new training opportunities.  Be the first to know by signing up for the Training Events Newsletter.

Virtual events are recorded and posted to PDB-101.  Watch 2024 events, including

• Teaching Enzymology with the Protein Data Bank: From Pandemic to Paxlovid (2024)

  In the second edition of this webinar, SARS-CoV-2 Main Protease is used to introduce and reinforce the use of RCSB.org resources for teaching protein structure and function.

• Understanding PDB Validation: Which experimental structures should I rely on?

Learn about primary PDB structure quality metrics, including those in the validation slider graphic; how PDB structure quality varies across the archive; and identify good structure(s) for research from RCSB.org.

• A Deep Dive into Computed Structure Model Exploration at RCSB.org

Learn how to use RCSB.org features to navigate 3D predicted protein structures in the context of experimentally-determined PDB structures. Two case studies are provided: Low-density Lipoprotein Receptor Adapter Protein 1 (LDLRAP1) and Class II aminoacyl-tRNA synthetases.

• Visualize Biomolecular Structures with Mol*: From Atoms to Movies

Mol* (MolStar) is a web application available on RCSB.org designed for visualizing biomolecular structures in 3D.

• Python Scripting for Molecular Docking | Part 3

In this workshop, Python scripting and libraries are used to explore ligand binding to enzymes. The corresponding Jupyter notebooks are customizable for individual research and teaching purposes. This course was developed by Paul A. Craig (Rochester Institute of Technology) and Jessica A. Nash (Molecular Sciences Software Institute).

In December, the 2024 Nobel Prize in Chemistry was awarded to David Baker for computational protein design and to Demis Hassabis and John M. Jumper for protein structure prediction.
Researchers have long used the wealth of experimentally-determined structures available from the open-access PDB archive to understand basic principles of protein architecture. More recently, PDB structures have been used as training data for Artificial Intelligence/Machine Learning software tools (e.g., AlphaFold, RosettaFold, OpenFold) that are able to predict three-dimensional structures of proteins and design proteins with novel shapes and biochemical functions (see the wwPDB announcement for more details).

• Visit PDB-101 to learn more about Protein Structure Prediction, Design, and Computed Structure Models in a new collection of resources.
• Read in Nature how pioneering crystallographer and RCSB PDB Director Emerita Helen Berman helped to set up the massive collection of protein structures that underpins the Nobel-prize-winning tool’s success

  The huge protein database that spawned AlphaFold and biology’s AI revolution Nature 2024 634:1028-1029. https://doi.org/10.1038/d41586-024-03423-0

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

• Summer internships for undergraduates in software development
• Gap Year Opportunities For Scientific Software Developers
• Postdocs and other open positions
• Training Events

The wwPDB Foundation awarded prizes for outstanding student presentations at several meetings:

The Protein Society Annual Symposium (Vancouver, Canada; July 23-26, 2024).

An Expanded Integrator Sensor Motif for GPCR Ligand Detection
Aubrey Putansu and Wenjing Wang, University of Michigan

The VI Latin American Crystallographic Association Meeting (Montevideo, Uruguay, September 23-26)

The Role of SEPT7 in Magnaporthe oryzae: Structural Insights and Functional Implications
Z Abbas (1), LAV Fernández (1), IA Cavini (2), DA Leonardo (1), RC Garratt (1)
(1)São Carlos Institute of Physics, University of São Paulo
(2)School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo

Many thanks to the meeting organizers and poster prize judges for making this award possible.

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: Dectris, Discngine, and Rigaku.

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

Visit PDB-101 to watch Target Zero, a documentary that shows the challenge and emotional complexity of the fight to control HIV infection. It features real-life patient stories, state of the art molecular animations based on PDB data, and interviews with medical professionals and scientists. These accounts illuminate the history of the HIV epidemic and reveal the ongoing need for compassionate, patient-centered care and a true understanding of the science behind the treatments.

This production was led by the RCSB PDB Director Emerita, Helen Berman and is a collaborative effort among scientists, physicians, patients, artists, and filmmakers based or trained at LAC+USC, the RCSB Protein Data Bank, Rutgers University, the University of Utah, and USC Cinema.

Molecular case studies (MCSs) are open educational resources that use a storytelling approach to engage students in biomolecular structure-function explorations, at the interface of biology and chemistry. Augmented reality (AR) is an interactive and engaging experience that has been used effectively in teaching molecular sciences.
Read about the incorporation of ready-to-use AR objects as checkpoints in the MCS. Interacting with these AR objects facilitated instructor preparation, reduced students’ cognitive load, and provided clear expectations for their learning.
Using augmented reality in molecular case studies to enhance biomolecular structure-function explorations in undergraduate classrooms

D. Vardar-Ulu, S.E. Ragab, S. Agrawal, S. Dutta
(2024) J Microbiol Biol Educ. 436: 168546 doi:10.1128/jmbe.00019-24