A New Chapter for RCSB Protein Data Bank Molecule of the Month in 2025

Biochemistry Life Sciences
Protein Data Bank Molecule of the Month Structural Biology Education Outreach Biomolecular Structures

Academic Background

The Protein Data Bank (PDB) is the most important global resource for three-dimensional structural data of biological molecules. Since its establishment in 1971, the PDB has become a vital tool in fields such as structural biology, biomedicine, bioenergy, and biotechnology. The PDB not only provides researchers with a vast amount of experimentally determined biomolecular structures but also supports educators in incorporating these structures into teaching, helping students understand the structure and function of biomolecules. However, with the rapid advancement of structural biology technologies, particularly cryo-electron microscopy (cryo-EM) and artificial intelligence (AI)-based protein structure prediction, the PDB faces new challenges: how to more effectively communicate the scientific significance of these complex structures to the public and researchers.

“Molecule of the Month” is the flagship feature of the PDB-101 educational platform. Since its inception in 2000 by David S. Goodsell, it has published over 300 articles, aiming to introduce important biomolecular structures and their functions in the PDB in an accessible manner. In 2025, Janet Iwasa succeeded Goodsell as the new editor-in-chief of the series, marking a new phase in the development of “Molecule of the Month.” This article will detail the background, significance, and future directions of this transition.

Source of the Paper

This paper is co-authored by Janet Iwasa, David S. Goodsell, Stephen K. Burley, and Christine Zardecki, who are affiliated with Rutgers University, Scripps Research Institute, and the RCSB Protein Data Bank, respectively. The paper was published on April 18, 2025, in the journal Structural Dynamics, titled “A New Chapter for RCSB Protein Data Bank Molecule of the Month in 2025.” It is part of a special series from the 74th Annual Meeting of the American Crystallographic Association, aimed at sharing the latest advances and educational achievements in structural science.

Main Content

1. History and Significance of the PDB and “Molecule of the Month”

The PDB is the only global public resource for three-dimensional structural data of biological molecules, currently hosting over 230,000 structures. Its users include structural biologists, researchers, and educators. As one of the partners of the Worldwide Protein Data Bank (wwPDB), the RCSB PDB is responsible for data storage, validation, and bioinformatics processing. Since its establishment in 2011, the PDB-101 platform has provided rich educational resources, including the “Molecule of the Month” series, videos, interactive animations, and curriculum materials.

The “Molecule of the Month” series helps readers understand the structure and function of biomolecules by reducing technical jargon, incorporating contextual stories, and showcasing dynamic processes. The series covers classic topics such as DNA and hemoglobin, as well as emerging technologies like cryo-EM and X-ray free-electron lasers (XFEL), and hot topics such as plastic-degrading enzymes and the H5N1 influenza virus.

2. Challenges and Opportunities of New Technologies

With the rapid development of cryo-EM and AI-based protein structure prediction technologies, the PDB faces new challenges. Cryo-EM can resolve the structures of large molecular complexes, but these structures often consist of multiple protein and nucleic acid chains, requiring a hierarchical approach for presentation. AI-predicted structure models (such as AlphaFold2 and RoseTTAFold) can predict three-dimensional structures from protein sequences, but their accuracy varies, and they typically do not include cofactors or ligands. These technologies provide new material for the “Molecule of the Month” series but also require authors to carefully explain the reliability of the models when telling their stories.

3. Janet Iwasa’s New Direction

Janet Iwasa published her inaugural article in January 2025, introducing the dynamic process of “assembly line-like” polyketide synthases. She used molecular animation to integrate multiple PDB structures into a coherent story, showcasing this complex process across multiple scales. While molecular animation can intuitively depict molecular dynamics, experimental data are often incomplete, requiring some degree of speculation. To mitigate uncertainty, Iwasa added textual explanations and visual cues to the animations.

4. Commitment to Open Access

The PDB has adhered to the principle of open access since its inception, and all educational resources on the PDB-101 platform are freely available for use and reuse. In 2024, the “Molecule of the Month” series was accessed 690,000 times by users worldwide, with articles on classic topics such as hemoglobin, collagen, and insulin remaining the most popular. Additionally, content related to COVID-19 was widely disseminated.

5. Plans for the Next 25 Years

David Goodsell led the “Molecule of the Month” series for the past 25 years, and in 2025, he passed the baton to Janet Iwasa. Moving forward, the series will continue to provide high-quality educational and outreach content through the PDB-101 platform, supporting research and education in structural biology.

Significance and Value

This paper not only reviews the history and achievements of the “Molecule of the Month” series but also looks ahead to its future development. With the advancement of structural biology technologies, the PDB-101 platform will continue to play a crucial role in research and education. Janet Iwasa’s involvement brings new energy to the series, and her molecular animation techniques will provide readers with a more intuitive and engaging scientific experience. Additionally, the PDB’s open-access policy ensures that these valuable resources are freely available to users worldwide, promoting the dissemination and application of scientific knowledge.

Highlights

  1. History and Legacy: This paper provides a detailed review of the 25-year history of the “Molecule of the Month” series, showcasing its important role in scientific communication and education.
  2. Challenges of New Technologies: The rapid development of cryo-EM and AI-based protein structure prediction presents new opportunities and challenges for the PDB. This paper delves into the impact of these technologies on scientific communication.
  3. Janet Iwasa’s Innovation: Janet Iwasa brings new vitality to the “Molecule of the Month” series with her molecular animation techniques. Her inaugural article on polyketide synthases offers readers a fresh scientific experience.
  4. Open Access: The PDB’s open-access policy ensures that these valuable resources are freely available to users worldwide, promoting the dissemination and application of scientific knowledge.

Conclusion

This paper reviews the history and achievements of the “Molecule of the Month” series and looks ahead to its future development. With the advancement of structural biology technologies, the PDB-101 platform will continue to play a crucial role in research and education. Janet Iwasa’s involvement brings new energy to the series, and her molecular animation techniques will provide readers with a more intuitive and engaging scientific experience. Additionally, the PDB’s open-access policy ensures that these valuable resources are freely available to users worldwide, promoting the dissemination and application of scientific knowledge.