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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 - Nonadditivity in public and inhouse data: implications for drug design

Numerous ligand-based drug discovery projects are based on structure-activity relationship (SAR) analysis, such as Free-Wilson (FW) or matched molecular pair (MMP) analysis. Intrinsically they assume linearity and additivity of substituent contributions. These techniques are challenged by nonadditivity (NA) in protein–ligand binding where the change of two functional groups in one molecule results in much higher or lower activity than expected from the respective single changes. Identifying nonlinear cases and possible underlying explanations is crucial for a drug design project since it might influence which lead to follow. By systematically analyzing all AstraZeneca (AZ) inhouse compound data and publicly available ChEMBL25 bioactivity data, the authors show significant NA events in almost every second assay among the inhouse and once in every third assay in public data sets. Furthermore, 9.4% of all compounds of the AZ database and 5.1% from public sources display significant additivity shifts indicating important SAR features or fundamental measurement errors. Using NA data in combination with machine learning showed that nonadditive data is challenging to predict and even the addition of nonadditive data into training did not result in an increase in predictivity. Overall, NA analysis should be applied on a regular basis in many areas of computational chemistry and can further improve rational drug design.

This article is first in our new article collection "Biomedical Data Analyses Facilitated by Open Cheminformatics Workflows"

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

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

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.

Featured Collection - Big Data in Chemistry

The increasing volume of biomedical data in chemistry and life sciences requires the development of new methodologies and approaches for their analysis. Artificial intelligence (AI) and machine learning, especially neural networks, are increasingly used in the chemical industry, in particular with respect to big data. The collection presents progress and exemplifies the current needs, trends and requirements for machine learning in chemical data analysis.

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.

COVID-19 and peer review

As a result of the significant disruption that is being caused by the COVID-19 pandemic we are very aware that many researchers will have difficulty in meeting the timelines associated with our peer review process during normal times. Please do let us know if you need additional time. Our systems will continue to remind you of the original timelines but we intend to be highly flexible at this time.

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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Editor profiles

Editors-in-Chief:

New Content ItemEgon Willighagen is a researcher in the BiGCaT Department for Bioinformatics and teacher at Maastricht University in the Netherlands.
 

New Content ItemRajarshi Guha is the Associate Director of Informatics at Vertex Pharmaceuticals, USA, where he leads the cheminformatics group that is responsible for informatics needs in high throughput screening.

Associate Editors:

New Content ItemNina Jeliazkova is a founder and co-owner of Ideaconsult Ltd, Bulgaria, and has been technical manager of the company since 2009.


New Content ItemBarbara Zdrazil is a group leader at the University of Vienna, Austria, and works as a safety data scientist for the European Bioinformatics Institute (EMBL-EBI), UK.

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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