Journal of Cheminformatics

Featured article: TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data

Owing to the increase in freely available software and data for cheminformatics and structural bioinformatics, research for computer-aided drug design (CADD) is more and more built on modular, reproducible, and easy-to-share pipelines. While documentation for such tools is available, there are only a few freely accessible examples that teach the underlying concepts focused on CADD, especially addressing users new to the field. In this article, Sydow et al. present TeachOpenCADD, a teaching platform developed by students for students, using open source compound and protein data as well as basic and CADD-related Python packages. We provide interactive Jupyter notebooks for central CADD topics, integrating theoretical background and practical code.

Content type: Commentary
| 14 October 2019

A path to next-generation reproducibility in cheminformatics

Authors: Robert D. Clark
Content type: Methodology
| 24 September 2019

A general approach for retrosynthetic molecular core analysis

Authors: J. Jesús Naveja, B. Angélica Pilón-Jiménez, Jürgen Bajorath and José L. Medina-Franco
Content type: Research article
| 18 September 2019

Open-source QSAR models for pKa prediction using multiple machine learning approaches

Authors: Kamel Mansouri, Neal F. Cariello, Alexandru Korotcov, Valery Tkachenko, Chris M. Grulke, Catherine S. Sprankle, David Allen, Warren M. Casey, Nicole C. Kleinstreuer and Antony J. Williams
Content type: Research article
| 11 September 2019

Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies

Authors: Christoph A. Bauer, Gisbert Schneider and Andreas H. Göller
Content type: Research article
| 30 August 2019

SAR and QSAR modeling of a large collection of LD₅₀ rat acute oral toxicity data

Authors: Domenico Gadaleta, Kristijan Vuković, Cosimo Toma, Giovanna J. Lavado, Agnes L. Karmaus, Kamel Mansouri, Nicole C. Kleinstreuer, Emilio Benfenati and Alessandra Roncaglioni

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2019

Proceedings of the 11th International Conference on Chemical Structures
Edited by Gerard van Westen and Markus Wagener
Collection published: 14 February 2019

Programming Languages for Chemical Information
Edited by Rajarshi Guha
Collection published: 5 February 2019

2018

BioCreative V.5
Edited by Martin Krallinger, Obdulia Rabal, Anália Lourenço, Alfonso Valencia
Collection published: 14 December 2018

Novel applications of machine learning in cheminformatics
Edited by Ola Spjuth
Collection published: 21 February 2018

2015

Cross journal collection
Jean-Claude Bradley Memorial Series
Edited by Andrew SID Lang, Antony Williams
Collection published: 22 March 2015

2013

6th Joint Sheffield Conference on Chemoinformatics
Collection published: 29 July 2013

2012

The IUPAC International Chemical Identifier (InChI) and its influence on the domain of chemical information
Edited by Antony Williams
Collection published: 13 December 2012

Semantic physical science
Edited by Henry Rzepa, Peter Murray-Rust
Collection published: 3 August 2012

2011

Visions of a semantic molecular future
Collection published: 14 October 2011

RDF technologies in chemistry
Edited by Egon Willighagen, Martin Paul Braendle
Collection published: 13 May 2011

PubChem3D
Collection published: 27 January 2011

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

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New Thematic Series: Programming Languages for Chemical Information

Cheminformatics methods and analyses employ software written in different programming languages, with each one offering features that make it more or less suitable for a given task. While there is much research on programming languages, we believe it would be useful for practitioners to report on how their preferred language has benefited them in practice.

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

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

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Nina Jeliazkova, Idea Consult Ltd., Bulgaria

Journal of Cheminformatics

Featured article: TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data

Articles

A path to next-generation reproducibility in cheminformatics

A general approach for retrosynthetic molecular core analysis

Open-source QSAR models for pKa prediction using multiple machine learning approaches

Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies

SAR and QSAR modeling of a large collection of LD₅₀ rat acute oral toxicity data

2019

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2015

2013

2012

2011

Upcoming Special Issues

Aims and Scope

New Thematic Series: Programming Languages for Chemical Information

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