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Welcome

Journal of CheminformaticsJournal of Cheminformatics is an open-access journal publishing original peer-reviewed research in all aspects of cheminformatics and molecular modelling.

Featured article - MolData, a molecular benchmark for disease and target based machine learning

Deep learning’s automatic feature extraction has been a revolutionary addition to computational drug discovery, infusing both the capabilities of learning abstract features and discovering complex molecular patterns via learning from molecular data. Since biological and chemical knowledge are necessary for overcoming the challenges of data curation, balancing, training, and evaluation, it is important for databases to contain information regarding the exact target and disease of each bioassay. The existing depositories such as PubChem or ChEMBL offer the screening data for millions of molecules against a variety of cells and targets, however, their bioassays contain complex biological descriptions which can hinder their usage by the machine learning community. In this work, a comprehensive disease and target-based dataset is collected from PubChem in order to facilitate and accelerate molecular machine learning for better drug discovery. MolData is one the largest efforts to date for democratizing the molecular machine learning, with roughly 170 million drug screening results from 1.4 million unique molecules assigned to specific diseases and targets. It also provides 30 unique categories of targets and diseases. Correlation analysis of the MolData bioassays unveils valuable information for drug repurposing for multiple diseases including cancer, metabolic disorders, and infectious diseases. Finally, the authors provide a benchmark of more than 30 models trained on each category using multitask learning. MolData aims to pave the way for computational drug discovery and accelerate the advancement of molecular artificial intelligence in a practical manner.

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

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

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.

Benefit from our free funding service

We offer a free open access support service to make it easier for you to discover and apply for article-processing charge (APC) funding.

Learn more here.

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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. 

Citation Typing Ontology (CiTO) Pilot

The Journal of Cheminformatics is piloting use of the Citation Typing Ontology (CiTO) in its papers. Any author wishing to submit to the journal is free to participate in the pilot. To learn more about how, please click through to our dedicated page on the CiTO pilot and to see published papers already participating in the pilot.

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Annual Journal Metrics

  • Speed (average)
    47 days to first decision for reviewed manuscripts only
    32 days to first decision for all manuscripts
    124 days from submission to acceptance
    16 days from acceptance to publication

    Usage 
    760,938 downloads
    1567 Altmetric mentions

    Citations
    Click here to see citation distribution in recent years