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Featured article: a new semi-automated workflow for chemical data retrieval and quality checking for modeling applications

The quality of data used for QSAR model derivation is extremely important as it strongly affects the final robustness and predictive power of the model. Ambiguous or wrong structures need to be carefully checked, because they lead to errors in calculation of descriptors, hence leading to meaningless results. The increasing amounts of data, however, have often made it hard to check of very large databases manually. In this paper, the authors designed and implemented a semi-automated workflow integrating structural data retrieval from several web-based databases, automated comparison of these data, chemical structure cleaning, selection and standardization of data into a consistent, ready-to-use format that can be employed for modeling.​​​​​​​

Articles

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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Aims and Scope

Journal of CheminformaticsJournal 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

Programming LanguagesCheminformatics 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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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 where he leads the cheminformatics group that is responsible for informatics needs in high throughput screening.​​​​​​​

Associate Editor:

Nina Jeliazkova, Idea Consult Ltd., Bulgaria

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