Beyond performance: how design choices shape chemical language models
Authors: Inken Fender, Jannik Adrian Gut and Thomas Lemmin
Content type: Research
18 November 2025
Welcome
Journal of CheminformaticsJournal of Cheminformatics is an open-access journal publishing original peer-reviewed research in all aspects of cheminformatics and molecular modelling.
Collection open to submissions
Evaluating AI and machine learning models in cheminformatics: benchmarking techniques and case studies
This collection aims to advance the field by presenting benchmarking methodologies and case studies that highlight the use of AI and machine learning models in cheminformatics. We seek contributions that provide detailed evaluations of computational tools, innovative benchmarking frameworks, and comprehensive case studies demonstrating the effectiveness of these models in predicting chemical properties.
Featured article
From molecules to data: the emerging impact of chemoinformatics in chemistry
Chemoinformatics is a rapidly advancing field that integrates chemistry, computer science, and data analysis to enhance the study and application of chemical systems. This interdisciplinary approach leverages computational tools and large datasets to drive innovation in various chemical disciplines, including drug discovery, materials science, and environmental chemistry. Recent advancements in artificial intelligence (AI) and machine learning (ML) have significantly improved the ability to analyze complex datasets, predict molecular properties, and design new compounds.
Featured collections
A picture of a circuit board © Michael Schwarzenberger from Pixabay (CC0)Milestones in Cheminformatics
This special collection of commentaries is introduced for celebrating the 15th anniversary of the Journal of Cheminformatics. Pioneers and experts presents the greatest of all concepts, methodologies, and developments that have pushed the boundaries of cheminformatics to its current form, as well as forthcoming challenges and opportunities.
New Content Item © Pietro Jeng on UnsplashAI in Drug Discovery
The dramatic increase in the use of Artificial Intelligence (AI) and traditional machine learning methods in different scientific fields has become an essential asset in the future development of the chemical industry, including the pharmaceutical, agro biotech, and other chemical sectors. This collection discusses about the cutting-edge contributions in the rapidly evolving field of AI-driven drug discovery.
Articles
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NPBS Atlas: a comprehensive data resource for exploring the biological sources of natural products
Authors: Tingjun Xu, Jinfang Dai, Yingyong Li, Junhong Zhou, Yingli Zhao, Weiming Chen and Xiao-Song Xue
Content type: Database 18 November 2025 -
Enhancing multi-task in vivo toxicity prediction via integrated knowledge transfer of chemical knowledge and in vitro toxicity information
Authors: Minsu Park, Yewon Shin, Hyunho Kim and Hojung Nam
Content type: Research 12 November 2025 -
Predicting the critical micelle concentration of binary surfactant mixtures using machine learning
Authors: Aditya Choudhary, Saaketh Desai, Methun Kamruzzaman, Alexander Landera, Koushik Ghosh and Kunal Poorey
Content type: Research 12 November 2025 -
How evaluation choices distort the outcome of generative drug discovery
Authors: Rıza Özçelik and Francesca Grisoni
Content type: Research 12 November 2025
2025
Evaluating AI and machine learning models in cheminformatics: benchmarking techniques and case studies
Open for submission
Research from the 13th International Conference on Chemical Structures
Open for submission
2024
Milestones in Cheminformatics
Closed. This collection is no longer accepting submissions.
AI in Drug Discovery
Closed. This collection is no longer accepting submissions.
2023
Research from the Ninth Joint Sheffield Conference on Chemoinformatics
Started publishing: 21 December 2023
Improving Reproducibility and Reusability in the Journal of Cheminformatics
Started publishing: 30 June 2023
2022
Research from 12th International Conference on Chemical Structures
Started publishing: 3 October 2022
Diversifying cheminformatics
Started publishing: 2 August 2022
2021
Biomedical Data Analyses Facilitated by Open Cheminformatics Workflows
Edited by Eva Nittinger, Alex Clark, Anna Gaulton, Barbara Zdrazil
Started publishing: 2 July 2021
2020
In Silico Structure Generation: Recent Developments, Applications, and Challenges
Edited by José L. Medina-Franco, Emma Schymanski, Christoph Steinbeck
Started publishing: 27 October 2020
Citation Typing Ontology (CiTO) Pilot
Edited by Egon Willighagen
Started publishing: 28 July 2020
2019
Big Data in Chemistry
Edited by Igor V. Tetko
Started publishing: 8 August 2019
Proceedings of the 11th International Conference on Chemical Structures
Edited by Gerard van Westen and Markus Wagener
Started publishing: 14 February 2019
Programming Languages for Chemical Information
Edited by Rajarshi Guha
Started publishing: 5 February 2019
2018
BioCreative V.5
Edited by Martin Krallinger, Obdulia Rabal, Anália Lourenço, Alfonso Valencia
Started publishing: 14 December 2018
Novel applications of machine learning in cheminformatics
Edited by Ola Spjuth
Started publishing: 21 February 2018
2015
Cross journal collection
Jean-Claude Bradley Memorial Series
Edited by Andrew SID Lang, Antony Williams
Started publishing: 22 March 2015
2013
6th Joint Sheffield Conference on Chemoinformatics
Started publishing: 29 July 2013
2012
The IUPAC International Chemical Identifier (InChI) and its influence on the domain of chemical information
Edited by Antony Williams
Started publishing: 13 December 2012
Semantic physical science
Edited by Henry Rzepa, Peter Murray-Rust
Started publishing: 3 August 2012
2011
Visions of a semantic molecular future
Started publishing: 14 October 2011
RDF technologies in chemistry
Edited by Egon Willighagen, Martin Paul Braendle
Started publishing: 13 May 2011
PubChem3D
Started publishing: 27 January 2011
2023
Improving reproducibility and reusability in the Journal of Cheminformatics
Charles Tapley Hoyt, Barbara Zdrazil, Rajarshi Guha, Nina Jeliazkova, Karina Martinez-Mayorga & Eva Nittinger
30 June 2023
Are new ideas harder to find? A note on incremental research and Journal of Cheminformatics’ Scientific Contribution Statement
Barbara Zdrazil, Rajarshi Guha, Karina Martinez-Mayorga & Nina Jeliazkova
15 January 2024
Biomedical data analyses facilitated by open cheminformatics workflows
Eva Nittinger, Alex Clark, Anna Gaulton & Barbara Zdrazil
17 April 2023
A look back at a pilot of the citation typing ontology
Rajarshi Guha, Barbara Zdrazil, Nina Jeliazkova & Karina Martinez-Mayorga
3 February 2023
2022
Diversifying cheminformatics
Barbara Zdrazil and Rajarshi Guha
25 April 2022
2021
What is the role of cheminformatics in a pandemic?
Rajarshi Guha, Egon Willighagen, Barbara Zdrazil & Nina Jeliazkova
2 March 2021
2020
From Big Data to Artificial Intelligence: chemoinformatics meets new challenges
Igor V. Tetko & Ola Engkvist
18 December 2020
Adoption of the Citation Typing Ontology by the Journal of Cheminformatics
Egon Willighagen
28 July 2020
Learning cheminformatics
Rajarshi Guha & Egon Willighagen
20 January 2020
2019
Journal of Cheminformatics, ORCID, and GitHub
Egon Willighagen, Nina Jeliazkova & Rajarshi Guha
8 July 2019
Implementing cheminformatics
Rajarshi Guha
5 February 2019
2018
Novel applications of Machine Learning in cheminformatics
Ola Spjuth
6 September 2018
2017
Helping to improve the practice of cheminformatics
Rajarshi Guha & Egon Willighagen
2013
Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians
David J Wild
5 July 2013
2012
InChI: connecting and navigating chemistry
Antony J Williams
13 December 2012
Semantic physical science
Peter Murray-Rust & Henry S Rzepa
3 August 2012
2011
Semantic science and its communication - a personal view
Peter Murray-Rust
14 October 2011
Resource description framework technologies in chemistry
Egon L Willighagen & Martin P Brändle
13 May 2011
2009
Grand challenges for cheminformatics
David J Wild
Journal announcements
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Annual Journal Metrics
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Citation Impact
Journal Impact Factor: 5.7 (2024)
5-year Journal Impact Factor: 8.9 (2024)
Source Normalized Impact per Paper (SNIP): 1.792 (2024)
SCImago Journal Rank (SJR): 1.570 (2024)Speed
Submission to first editorial decision (median days): 9
Submission to acceptance (median days): 131
Usage 2024
Downloads: 1,615,511
Altmetric mentions: 886Citations
Click here to see citation distribution in recent years -