Milestones in cheminformatics

Abstract

The field of cheminformatics has undergone significant transformation since its inception, evolving from a niche discipline to a cornerstone of modern medicinal chemistry, pharmaceutical research, and several other areas of chemistry [1,2,3]. To celebrate the 15th anniversary of the Journal of Cheminformatics, we present the special collection Milestones in Cheminformatics, https://www.biomedcentral.com/collections/MICHE, showcasing how cheminformatics has grown into a key discipline underpinning chemical research, innovation, and applications. The collection is intended to serve not only as a retrospective view but also as a platform to envision the future directions of cheminformatics.

This special issue brings together perspectives from renowned scholars and practitioners who highlight transformative developments across various domains of cheminformatics. Bajorath offers a global perspective on the trajectory of the field, setting the stage for future integration and growth. Willett revisits the early efforts in chemical database search. Reymond highlights the conceptual and practical implications of chemical space as a unifying theme, offering insights into its role in visualizing diversity and guiding discovery. Tropsha and colleagues present a critical analysis of current paradigms for assessing the accuracy of QSAR models, arguing for more nuanced and task-specific validation strategies. Steinbeck traces the journey from closed systems to collaborative innovation, while Williams and Richard propose three pillars for ensuring public access and data integrity in chemical databases. Bienstock discusses the impact and potential of AI/ML methods in designing new chemical entities, underscoring their growing role in predictive modeling and virtual screening. Rather than a closing section, Varnek et al. touches an important aspect of the future by exploring achievements and challenges in higher education, emphasizing the need for structured cheminformatics curricula and interdisciplinary competencies.

Contributions in this collection illustrate the multidimensional character of cheminformatics—from its computational and theoretical foundations to its educational, ethical, and infrastructural components. The collection highlights both the progress achieved and the challenges that remain, such as harmonizing data standards, ensuring reproducibility, and fostering inclusive access to tools and knowledge [3], while also intersecting with disciplines like bioinformatics, materials science, and systems biology [4]. Transparency, collaboration, and interdisciplinary interactions are poised to become key drivers of future developments in the field. The rise of explainable artificial intelligence and sustainable data practices are likely to define the next era of cheminformatics.

The field of cheminformatics has been sculptured by many scientists—those who contributed to this special collection, those who were unable to do so at the time, and others whose legacy and ideas continue to live on in the literature. The very fact that we are celebrating the 15th anniversary of the Journal of Cheminformatics speaks volumes about the commitment and vision of the cheminformatics community. This special collection, Milestones in Cheminformatics, is expected to inform and inspire its readers in the years to come, while also honoring the broader community whose continued contributions shape the field.

Data availability statement is not applicable. This is an Editorial manuscript.

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We thank all the authors who contributed to this collection and to UNAM for funding. We also thank the reviewers for their feedback to the papers and the editorial team of the Journal of Cheminformatics for their support.

Authors and Affiliations

1. Institute of Chemistry, Campus Merida, National Autonomous University of Mexico, Merida-Tetiz Highway, Km. 4.5, Ucu, 97357, Yucatan, Mexico

   Karina Martinez-Mayorga

2. DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510, Mexico

   José L. Medina-Franco

Authors

1. Karina Martinez-MayorgaView author publications

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2. José L. Medina-FrancoView author publications

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Contributions

Both authors contributed equally to writing the manuscript.

Corresponding authors

Correspondence to Karina Martinez-Mayorga or José L. Medina-Franco.

Competing interests

The authors declare that they have no conflicts of interest.

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Martinez-Mayorga, K., Medina-Franco, J.L. Milestones in cheminformatics. J Cheminform 17, 104 (2025). https://doi.org/10.1186/s13321-025-01054-9

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• Published: 14 July 2025

• DOI: https://doi.org/10.1186/s13321-025-01054-9

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