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  1. In this work, we explore the potential of deep learning to streamline the process of identifying new potential drugs through the computational generation of molecules with interesting biological properties. Tw...

    Authors: Tiago Pereira, Maryam Abbasi, Bernardete Ribeiro and Joel P. Arrais

    Citation: Journal of Cheminformatics 2021 13:21

    Content type: Research article

    Published on:

  2. Chemistry looks back at many decades of publications on chemical compounds, their structures and properties, in scientific articles. Liberating this knowledge (semi-)automatically and making it available to th...

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

    Citation: Journal of Cheminformatics 2021 13:20

    Content type: Software

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  3. Compound (or chemical) databases are an invaluable resource for many scientific disciplines. Exposomics researchers need to find and identify relevant chemicals that cover the entirety of potential (chemical a...

    Authors: Emma L. Schymanski, Todor Kondić, Steffen Neumann, Paul A. Thiessen, Jian Zhang and Evan E. Bolton

    Citation: Journal of Cheminformatics 2021 13:19

    Content type: Research article

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  4. The development of selective inhibitors of the clinically relevant human Carbonic Anhydrase (hCA) isoforms IX and XII has become a major topic in drug research, due to their deregulation in several types of ca...

    Authors: Annachiara Tinivella, Luca Pinzi and Giulio Rastelli

    Citation: Journal of Cheminformatics 2021 13:18

    Content type: Research article

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  5. Enhanced/prolonged cAMP signalling has been suggested as a suppressor of cancer proliferation. Interestingly, two key modulators that elevate cAMP, the A2A receptor (A2AR) and phosphodiesterase 10A (PDE10A), are ...

    Authors: Leen Kalash, Ian Winfield, Dewi Safitri, Marcel Bermudez, Sabrina Carvalho, Robert Glen, Graham Ladds and Andreas Bender

    Citation: Journal of Cheminformatics 2021 13:17

    Content type: Research article

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  6. The process of drug discovery involves a search over the space of all possible chemical compounds. Generative Adversarial Networks (GANs) provide a valuable tool towards exploring chemical space and optimizing...

    Authors: Andrew E. Blanchard, Christopher Stanley and Debsindhu Bhowmik

    Citation: Journal of Cheminformatics 2021 13:14

    Content type: Research article

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  7. Malaria is a disease affecting hundreds of millions of people across the world, mainly in developing countries and especially in sub-Saharan Africa. It is the cause of hundreds of thousands of deaths each year...

    Authors: Nicolas Bosc, Eloy Felix, Ricardo Arcila, David Mendez, Martin R. Saunders, Darren V. S. Green, Jason Ochoada, Anang A. Shelat, Eric J. Martin, Preeti Iyer, Ola Engkvist, Andreas Verras, James Duffy, Jeremy Burrows, J. Mark F. Gardner and Andrew R. Leach

    Citation: Journal of Cheminformatics 2021 13:13

    Content type: Research article

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  8. Graph neural networks (GNN) has been considered as an attractive modelling method for molecular property prediction, and numerous studies have shown that GNN could yield more promising results than traditional...

    Authors: Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang, Chao Shen, Dongsheng Cao, Jian Wu and Tingjun Hou

    Citation: Journal of Cheminformatics 2021 13:12

    Content type: Research article

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  9. In this study, we developed a novel algorithm to improve the screening performance of an arbitrary docking scoring function by recalibrating the docking score of a query compound based on its structure similar...

    Authors: Beihong Ji, Xibing He, Yuzhao Zhang, Jingchen Zhai, Viet Hoang Man, Shuhan Liu and Junmei Wang

    Citation: Journal of Cheminformatics 2021 13:11

    Content type: Research article

    Published on:

  10. We present RegioSQM20, a new version of RegioSQM (Chem Sci 9:660, 2018), which predicts the regioselectivities of electrophilic aromatic substitution (EAS) reactions from the calculation of proton affinities. ...

    Authors: Nicolai Ree, Andreas H. Göller and Jan H. Jensen

    Citation: Journal of Cheminformatics 2021 13:10

    Content type: Research article

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  11. The ability of accurate predictions of biological response (biological activity/property/toxicity) of a given chemical makes the quantitative structure‐activity/property/toxicity relationship (QSAR/QSPR/QSTR) ...

    Authors: Agnieszka Gajewicz-Skretna, Supratik Kar, Magdalena Piotrowska and Jerzy Leszczynski

    Citation: Journal of Cheminformatics 2021 13:9

    Content type: Research article

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  12. ChemSpectra, a web-based software to visualize and analyze spectroscopic data, integrating solutions for infrared spectroscopy (IR), mass spectrometry (MS), and one-dimensional 1H and 13C NMR (proton and carbon n...

    Authors: Yu-Chieh Huang, Pierre Tremouilhac, An Nguyen, Nicole Jung and Stefan Bräse

    Citation: Journal of Cheminformatics 2021 13:8

    Content type: Software

    Published on:

  13. Protein solubility is significant in producing new soluble proteins that can reduce the cost of biocatalysts or therapeutic agents. Therefore, a computational model is highly desired to accurately predict prot...

    Authors: Jianwen Chen, Shuangjia Zheng, Huiying Zhao and Yuedong Yang

    Citation: Journal of Cheminformatics 2021 13:7

    Content type: Research article

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  14. Virtual screening (VS) based on molecular docking has emerged as one of the mainstream technologies of drug discovery due to its low cost and high efficiency. However, the scoring functions (SFs) implemented i...

    Authors: Xujun Zhang, Chao Shen, Xueying Guo, Zhe Wang, Gaoqi Weng, Qing Ye, Gaoang Wang, Qiaojun He, Bo Yang, Dongsheng Cao and Tingjun Hou

    Citation: Journal of Cheminformatics 2021 13:6

    Content type: Software

    Published on:

  15. The open rich-client Molecule Set Comparator (MSC) application enables a versatile and fast comparison of large molecule sets with a unique inter-set molecule-to-molecule mapping obtained e.g. by molecular-rec...

    Authors: Kohulan Rajan, Jan-Mathis Hein, Christoph Steinbeck and Achim Zielesny

    Citation: Journal of Cheminformatics 2021 13:5

    Content type: Preliminary communication

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  16. Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in N...

    Authors: Maria Sorokina, Peter Merseburger, Kohulan Rajan, Mehmet Aziz Yirik and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2021 13:2

    Content type: Database

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  17. Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processin...

    Authors: Rick Helmus, Thomas L. ter Laak, Annemarie P. van Wezel, Pim de Voogt and Emma L. Schymanski

    Citation: Journal of Cheminformatics 2021 13:1

    Content type: Software

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  18. An important task in cheminformatics is to test whether two molecules are equivalent with respect to their 2D structure. Mathematically, this amounts to solving the graph isomorphism problem for labelled graph...

    Authors: Jördis-Ann Schüler, Steffen Rechner and Matthias Müller-Hannemann

    Citation: Journal of Cheminformatics 2020 12:73

    Content type: Research article

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  19. 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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  20. 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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  21. 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

    Published on:

  22. 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

    Published on:

  23. 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

    Published on:

  24. 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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  25. 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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  26. 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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  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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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  33. 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

    Published on:

  34. 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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  35. 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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  36. 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

    Published on:

  37. 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

    Published on:

  38. 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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  39. 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

    Published on:

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