Journal of Cheminformatics is an open-access journal publishing original peer-reviewed research in all aspects of cheminformatics and molecular modelling.
Welcome
Featured article - Reinvent 4: Modern AI–driven generative molecule design
REINVENT 4 is a modern open-source generative AI framework for the design of small molecules. The software utilizes recurrent neural networks and transformer architectures to drive molecule generation. These generators are seamlessly embedded within the general machine learning optimization algorithms, transfer learning, reinforcement learning and curriculum learning. REINVENT 4 enables and facilitates de novo design, R-group replacement, library design, linker design, scaffold hopping and molecule optimization. This contribution gives an overview of the software and describes its design. Algorithms and their applications are discussed in detail. REINVENT 4 is a command line tool which reads a user configuration in either TOML or JSON format. The aim of this release is to provide reference implementations for some of the most common algorithms in AI based molecule generation. An additional goal with the release is to create a framework for education and future innovation in AI based molecular design.
Michael Schwarzenberger from Pixabay (CC0)
Featured Collection - In Silico Structure Generation: Recent Developments, Applications, and Challenges
This special collection showcases recent advances, applications, challenges in the enumeration of chemical structures: from the design to the analysis and use of either small, focused data sets, to large compound libraries. Analysis and handling of the newly constructed chemical structures include the storage, mining, integration of the constructed structures with other existing data sets, and curation.
Articles
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QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool
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Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1
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Comparative evaluation of methods for the prediction of protein–ligand binding sites
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Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning
2024
Milestones in Cheminformatics
Open for submission
AI in Drug Discovery
Open for submission
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
Upcoming Special Issues
Learn more about open Calls for Papers and upcoming Special Issues here.
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Pietro Jeng on Unsplash
Featured collection - Biomedical Data Analyses Facilitated by Open Cheminformatics Workflows
Modern data science approaches aim to properly interconnect information in order to generate new knowledge and reveal hidden relationships in the data. The open data revolution has given users explicit rights, via open licenses, to download, curate, and reshare results, leading to a democratization of data. This collection focuses on cheminformatics workflows licensed with an OSI-approved or Creative Commons license, serving the curation and analysis of diverse life science data sets.
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Annual Journal Metrics
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Citation Impact 2023
Journal Impact Factor: 7.1
5-year Journal Impact Factor: 9.3
Source Normalized Impact per Paper (SNIP): 2.078
SCImago Journal Rank (SJR): 1.745Speed 2023
Submission to first editorial decision (median days): 8
Submission to acceptance (median days): 116
Usage 2023
Downloads: 1,414,777
Altmetric mentions: 1,319Citations
Click here to see citation distribution in recent years -