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

Interaction fingerprints are vector representations that summarize the three-dimensional nature of interactions in molecular complexes, typically formed between a protein and a ligand. This kind of encoding has found many applications in drug-discovery projects, from structure-based virtual-screening to machine-learning. Here, the authors present ProLIF, a Python library designed to generate interaction fingerprints for molecular complexes extracted from molecular dynamics trajectories, experimental structures, and docking simulations. It can handle complexes formed of any combination of ligand, protein, DNA, or RNA molecules. The available interaction types can be fully reparametrized or extended by user-defined ones. Several tutorials that cover typical use-case scenarios are available, and the documentation is accompanied with code snippets showcasing the integration with other data-analysis libraries for a more seamless user-experience.

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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.

Authors: Jeff Guo, Jon Paul Janet, Matthias R. Bauer, Eva Nittinger, Kathryn A. Giblin, Kostas Papadopoulos, Alexey Voronov, Atanas Patronov, Ola Engkvist and Christian Margreitter

Content type: Research article

17 November 2021

Authors: Francois Berenger and Koji Tsuda

Content type: Research article

14 November 2021

Authors: Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng and Yuedong Yang

Content type: Research article

13 November 2021

Authors: Zi-Yi Yang, Li Fu, Ai-Ping Lu, Shao Liu, Ting-Jun Hou and Dong-Sheng Cao

Content type: Research article

13 November 2021

Authors: Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman and Gerard J. P. van Westen

Content type: Research article

12 November 2021

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Biomedical Data Analyses Facilitated by Open Cheminformatics Workflows
Edited byEva Nittinger, Alex Clark, Anna Gaulton, Barbara Zdrazil
Started publishing: 2 July 2021

In Silico Structure Generation: Recent Developments, Applications, and Challenges
Edited byJos茅 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

Big Data in Chemistry
Edited by Igor V. Tetko
Started publishing: 8 August 2019

Proceedings of the 11th International Conference on Chemical Structures
Edited byGerard van Westen and Markus Wagener
Started publishing: 14 February 2019

Programming Languages for Chemical Information
Edited by Rajarshi Guha
Started publishing:5 February 2019

BioCreative V.5
Edited byMartin Krallinger,Obdulia Rabal,An谩lia Louren莽o,Alfonso Valencia
Started publishing: 14 December 2018

Novel applications of machine learning in cheminformatics
Edited by Ola Spjuth
Started publishing: 21 February 2018

Cross journal collection
Jean-Claude Bradley Memorial Series
Edited byAndrew SID Lang,Antony Williams
Started publishing: 22 March 2015

6th Joint Sheffield Conference on Chemoinformatics
Started publishing: 29 July 2013

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

Visions of a semantic molecular future
Started publishing: 14 October 2011

RDF technologies in chemistry
Edited byEgon Willighagen, Martin Paul Braendle
Started publishing: 13 May 2011

PubChem3D
Started publishing: 27 January 2011

What is the role of cheminformatics in a pandemic?
Rajarshi Guha,Egon Willighagen, Barbara Zdrazil Nina Jeliazkova
2 March 2021

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 theJournal of Cheminformatics
Egon Willighagen
28 July 2020

Learning cheminformatics
Rajarshi GuhaEgon Willighagen
20 January2020

Journal of Cheminformatics, ORCID, and GitHub
Egon Willighagen,Nina JeliazkovaRajarshi Guha
8 July 2019

Implementing cheminformatics
Rajarshi Guha
5 February 2019

Novel applications of Machine Learning in cheminformatics
Ola Spjuth
6 September 2018

Helping to improve the practice of cheminformatics
Rajarshi GuhaEgon Willighagen

Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians
David J Wild
5 July 2013

InChI: connecting and navigating chemistry
Antony J Williams
13 December 2012

Semantic physical science
Peter Murray-RustHenry S Rzepa
3 August 2012

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 Br盲ndle
13 May 2011

Grand challenges for cheminformatics
David J Wild

Learn more about open Calls for Papers and upcoming Special Issues here.

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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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TheJournal of Cheminformaticsis piloting use of the Citation Typing Ontology (CiTO) in itspapers. 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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Egon Willighagenis aresearcher in the BiGCaT Department for Bioinformatics andteacher at Maastricht University in the Netherlands.

Rajarshi Guhais 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.

Nina Jeliazkovais a founder and co-owner of Ideaconsult Ltd, Bulgaria, and has been technical manager of the company since 2009.

Barbara Zdrazilis 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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