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  1. In the past two decades a lot of different formats for molecules and reactions have been created. These formats were mostly developed for the purposes of identifiers, representation, classification, analysis a...

    Authors: Victorien Delannée and Marc C. Nicklaus

    Citation: Journal of Cheminformatics 2020 12:72

    Content type: Research article

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  2. Biomedical information mining is increasingly recognized as a promising technique to accelerate drug discovery and development. Especially, integrative approaches which mine data from several (open) data sourc...

    Authors: Alzbeta Tuerkova and Barbara Zdrazil

    Citation: Journal of Cheminformatics 2020 12:71

    Content type: Educational

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  3. We present the open-source AiZynthFinder software that can be readily used in retrosynthetic planning. The algorithm is based on a Monte Carlo tree search that recursively breaks down a molecule to purchasable...

    Authors: Samuel Genheden, Amol Thakkar, Veronika Chadimová, Jean-Louis Reymond, Ola Engkvist and Esben Bjerrum

    Citation: Journal of Cheminformatics 2020 12:70

    Content type: Software

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  4. Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove th...

    Authors: Jonas Schaub, Achim Zielesny, Christoph Steinbeck and Maria Sorokina

    Citation: Journal of Cheminformatics 2020 12:67

    Content type: Research article

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  5. The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in Structure–Activity Relationship (SAR)-based chemical class...

    Authors: Gabriel Idakwo, Sundar Thangapandian, Joseph Luttrell, Yan Li, Nan Wang, Zhaoxian Zhou, Huixiao Hong, Bei Yang, Chaoyang Zhang and Ping Gong

    Citation: Journal of Cheminformatics 2020 12:66

    Content type: Research article

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  6. The automatic recognition of chemical structure diagrams from the literature is an indispensable component of workflows to re-discover information about chemicals and to make it available in open-access databa...

    Authors: Kohulan Rajan, Achim Zielesny and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2020 12:65

    Content type: Preliminary communication

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  7. Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases. This paper aims to examine the fundamental concepts of library...

    Authors: Fernanda I. Saldívar-González, C. Sebastian Huerta-García and José L. Medina-Franco

    Citation: Journal of Cheminformatics 2020 12:64

    Content type: Educational

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  8. Identifying and assessing ligand-target binding is a core component in early drug discovery as one or more unwanted interactions may be associated with safety issues.

    Authors: Laeeq Ahmed, Hiba Alogheli, Staffan Arvidsson McShane, Jonathan Alvarsson, Arvid Berg, Anders Larsson, Wesley Schaal, Erwin Laure and Ola Spjuth

    Citation: Journal of Cheminformatics 2020 12:62

    Content type: Methodology

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  9. The maximum common property similarity (MCPhd) method is presented using descriptors as a new approach to determine the similarity between two chemical compounds or molecular graphs. This method uses the conce...

    Authors: Aurelio Antelo-Collado, Ramón Carrasco-Velar, Nicolás García-Pedrajas and Gonzalo Cerruela-García

    Citation: Journal of Cheminformatics 2020 12:61

    Content type: Research article

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  10. Structural information about chemical compounds is typically conveyed as 2D images of molecular structures in scientific documents. Unfortunately, these depictions are not a machine-readable representation of ...

    Authors: Kohulan Rajan, Henning Otto Brinkhaus, Achim Zielesny and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2020 12:60

    Content type: Review

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  11. Recently, deep learning has been successfully applied to molecular graph generation. Nevertheless, mitigating the computational complexity, which increases with the number of nodes in a graph, has been a major...

    Authors: Youngchun Kwon, Dongseon Lee, Youn-Suk Choi, Kyoham Shin and Seokho Kang

    Citation: Journal of Cheminformatics 2020 12:58

    Content type: Research article

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  12. Named Entity Linking systems are a powerful aid to the manual curation of digital libraries, which is getting increasingly costly and inefficient due to the information overload. Models based on the Personaliz...

    Authors: Pedro Ruas, Andre Lamurias and Francisco M. Couto

    Citation: Journal of Cheminformatics 2020 12:57

    Content type: Research article

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  13. The objective of this work is to design a molecular generator capable of exploring known as well as unfamiliar areas of the chemical space. Our method must be flexible to adapt to very different problems. Ther...

    Authors: Jules Leguy, Thomas Cauchy, Marta Glavatskikh, Béatrice Duval and Benoit Da Mota

    Citation: Journal of Cheminformatics 2020 12:55

    Content type: Research article

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  14. This paper is a tutorial developed for the data analysis platform Galaxy. The purpose of Galaxy is to make high-throughput computational data analysis, such as molecular dynamics, a structured, reproducible an...

    Authors: Simon A. Bray, Tharindu Senapathi, Christopher B. Barnett and Björn A. Grüning

    Citation: Journal of Cheminformatics 2020 12:54

    Content type: Educational

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  15. We address the problem of generating novel molecules with desired interaction properties as a multi-objective optimization problem. Interaction binding models are learned from binding data using graph convolut...

    Authors: Yash Khemchandani, Stephen O’Hagan, Soumitra Samanta, Neil Swainston, Timothy J. Roberts, Danushka Bollegala and Douglas B. Kell

    Citation: Journal of Cheminformatics 2020 12:53

    Content type: Research article

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  16. In computer-assisted synthesis planning (CASP) programs, providing as many chemical synthetic routes as possible is essential for considering optimal and alternative routes in a chemical reaction network. As t...

    Authors: Ryosuke Shibukawa, Shoichi Ishida, Kazuki Yoshizoe, Kunihiro Wasa, Kiyosei Takasu, Yasushi Okuno, Kei Terayama and Koji Tsuda

    Citation: Journal of Cheminformatics 2020 12:52

    Content type: Preliminary communication

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  17. The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to...

    Authors: A. Patrícia Bento, Anne Hersey, Eloy Félix, Greg Landrum, Anna Gaulton, Francis Atkinson, Louisa J. Bellis, Marleen De Veij and Andrew R. Leach

    Citation: Journal of Cheminformatics 2020 12:51

    Content type: Methodology

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  18. Machine translation of chemical nomenclature has considerable application prospect in chemical text data processing between languages. However, rule based machine translation tools have to face significant com...

    Authors: Tingjun Xu, Weiming Chen, Junhong Zhou, Jingfang Dai, Yingyong Li and Yingli Zhao

    Citation: Journal of Cheminformatics 2020 12:50

    Content type: Research article

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  19. Root mean square displacement (RMSD) calculations play a fundamental role in the comparison of different conformers of the same ligand. This is particularly important in the evaluation of protein-ligand dockin...

    Authors: Rocco Meli and Philip C. Biggin

    Citation: Journal of Cheminformatics 2020 12:49

    Content type: Software

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  20. We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the...

    Authors: Dmytro G. Krotko

    Citation: Journal of Cheminformatics 2020 12:48

    Content type: Research article

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  21. Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs and discovering therapies for untreated diseases. Drug repositioning, therefore, plays an important role in opti...

    Authors: Tamer N. Jarada, Jon G. Rokne and Reda Alhajj

    Citation: Journal of Cheminformatics 2020 12:46

    Content type: Review

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  22. Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyt...

    Authors: Gerard Baquer, Lluc Sementé, María García-Altares, Young Jin Lee, Pierre Chaurand, Xavier Correig and Pere Ràfols

    Citation: Journal of Cheminformatics 2020 12:45

    Content type: Research article

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  23. In silico prediction of drug–target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. How...

    Authors: Maha A. Thafar, Rawan S. Olayan, Haitham Ashoor, Somayah Albaradei, Vladimir B. Bajic, Xin Gao, Takashi Gojobori and Magbubah Essack

    Citation: Journal of Cheminformatics 2020 12:44

    Content type: Research article

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  24. With the rise of artificial intelligence (AI) in drug discovery, de novo molecular generation provides new ways to explore chemical space. However, because de novo molecular generation methods rely on abundant...

    Authors: Xuanyi Li, Yinqiu Xu, Hequan Yao and Kejiang Lin

    Citation: Journal of Cheminformatics 2020 12:42

    Content type: Research article

    Published on:

  25. Affinity fingerprints report the activity of small molecules across a set of assays, and thus permit to gather information about the bioactivities of structurally dissimilar compounds, where models based on ch...

    Authors: Isidro Cortés-Ciriano, Ctibor Škuta, Andreas Bender and Daniel Svozil

    Citation: Journal of Cheminformatics 2020 12:41

    Content type: Research article

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  26. Here, we introduce the ChemicalToolbox, a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading,...

    Authors: Simon A. Bray, Xavier Lucas, Anup Kumar and Björn A. Grüning

    Citation: Journal of Cheminformatics 2020 12:40

    Content type: Software

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  27. An affinity fingerprint is the vector consisting of compound’s affinity or potency against the reference panel of protein targets. Here, we present the QAFFP fingerprint, 440 elements long in silico QSAR-based...

    Authors: C. Škuta, I. Cortés-Ciriano, W. Dehaen, P. Kříž, G. J. P. van Westen, I. V. Tetko, A. Bender and D. Svozil

    Citation: Journal of Cheminformatics 2020 12:39

    Content type: Research article

    Published on:

  28. Molecular generative models trained with small sets of molecules represented as SMILES strings can generate large regions of the chemical space. Unfortunately, due to the sequential nature of SMILES strings, t...

    Authors: Josep Arús-Pous, Atanas Patronov, Esben Jannik Bjerrum, Christian Tyrchan, Jean-Louis Reymond, Hongming Chen and Ola Engkvist

    Citation: Journal of Cheminformatics 2020 12:38

    Content type: Research article

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  29. For kinase inhibitors, X-ray crystallography has revealed different types of binding modes. Currently, more than 2000 kinase inhibitors with known binding modes are available, which makes it possible to derive...

    Authors: Raquel Rodríguez-Pérez, Filip Miljković and Jürgen Bajorath

    Citation: Journal of Cheminformatics 2020 12:36

    Content type: Research article

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  30. The development of drugs is often hampered due to off-target interactions leading to adverse effects. Therefore, computational methods to assess the selectivity of ligands are of high interest. Currently, sele...

    Authors: Lindsey Burggraaff, Herman W. T. van Vlijmen, Adriaan P. IJzerman and Gerard J. P. van Westen

    Citation: Journal of Cheminformatics 2020 12:33

    Content type: Research article

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  31. Deep learning is developing as an important technology to perform various tasks in cheminformatics. In particular, graph convolutional neural networks (GCNs) have been reported to perform well in many types of...

    Authors: Ryosuke Kojima, Shoichi Ishida, Masateru Ohta, Hiroaki Iwata, Teruki Honma and Yasushi Okuno

    Citation: Journal of Cheminformatics 2020 12:32

    Content type: Software

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  32. The spectroscopy of diatomic molecules is an important research area in chemical physics due to its relevance in astrochemistry, combustion chemistry, and ultracold physics. However, there is currently no data...

    Authors: Xiangyue Liu, Stefan Truppe, Gerard Meijer and Jesús Pérez-Ríos

    Citation: Journal of Cheminformatics 2020 12:31

    Content type: Database

    Published on:

  33. Aromatic rings are important residues for biological interactions and appear to a large extent as part of protein–drug and protein–protein interactions. They are relevant for both protein stability and molecul...

    Authors: Esteban Lanzarotti, Lucas A. Defelipe, Marcelo A. Marti and Adrián G. Turjanski

    Citation: Journal of Cheminformatics 2020 12:30

    Content type: Research article

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  34. MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment (Dissipative Particle) Dynamics. The new environme...

    Authors: Karina van den Broek, Mirco Daniel, Matthias Epple, Jan-Mathis Hein, Hubert Kuhn, Stefan Neumann, Andreas Truszkowski and Achim Zielesny

    Citation: Journal of Cheminformatics 2020 12:29

    Content type: Software

    Published on:

  35. Artificial intelligence (AI) is undergoing a revolution thanks to the breakthroughs of machine learning algorithms in computer vision, speech recognition, natural language processing and generative modelling. ...

    Authors: Noé Sturm, Andreas Mayr, Thanh Le Van, Vladimir Chupakhin, Hugo Ceulemans, Joerg Wegner, Jose-Felipe Golib-Dzib, Nina Jeliazkova, Yves Vandriessche, Stanislav Böhm, Vojtech Cima, Jan Martinovic, Nigel Greene, Tom Vander Aa, Thomas J. Ashby, Sepp Hochreiter…

    Citation: Journal of Cheminformatics 2020 12:26

    Content type: Research article

    Published on:

  36. Risk assessment of newly synthesised chemicals is a prerequisite for regulatory approval. In this context, in silico methods have great potential to reduce time, cost, and ultimately animal testing as they mak...

    Authors: Andrea Morger, Miriam Mathea, Janosch H. Achenbach, Antje Wolf, Roland Buesen, Klaus-Juergen Schleifer, Robert Landsiedel and Andrea Volkamer

    Citation: Journal of Cheminformatics 2020 12:24

    Content type: Research article

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  37. We report on a new cheminformatics enumeration technology—SIME, synthetic insight-based macrolide enumerator—a new and improved software technology. SIME can enumerate fully assembled macrolides with synthetic...

    Authors: Phyo Phyo Kyaw Zin, Gavin Williams and Denis Fourches

    Citation: Journal of Cheminformatics 2020 12:23

    Content type: Research article

    Published on:

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