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  1. Interpretation of QSAR models is useful to understand the complex nature of biological or physicochemical processes, guide structural optimization or perform knowledge-based validation of QSAR models. Highly p...

    Authors: Mariia Matveieva and Pavel Polishchuk
    Citation: Journal of Cheminformatics 2021 13:41
  2. The software for the IUPAC Chemical Identifier, InChI, is extraordinarily reliable. It has been tested on large databases around the world, and has proved itself to be an essential tool in the handling and int...

    Authors: Jonathan M. Goodman, Igor Pletnev, Paul Thiessen, Evan Bolton and Stephen R. Heller
    Citation: Journal of Cheminformatics 2021 13:40
  3. Deep generative models have shown the ability to devise both valid and novel chemistry, which could significantly accelerate the identification of bioactive compounds. Many current models, however, use molecul...

    Authors: Morgan Thomas, Robert T. Smith, Noel M. O’Boyle, Chris de Graaf and Andreas Bender
    Citation: Journal of Cheminformatics 2021 13:39
  4. The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF ...

    Authors: Jakub Galgonek and Jiří Vondrášek
    Citation: Journal of Cheminformatics 2021 13:38
  5. South African Natural Compounds Database (SANCDB; https://​sancdb.​rubi.​ru.​ac.​za/​) is the sole and a fully referenced database of natural chemical compounds of...

    Authors: Bakary N’tji Diallo, Michael Glenister, Thommas M. Musyoka, Kevin Lobb and Özlem Tastan Bishop
    Citation: Journal of Cheminformatics 2021 13:37
  6. Virtual screening, which can computationally predict the presence or absence of protein–compound interactions, has attracted attention as a large-scale, low-cost, and short-term search method for seed compound...

    Authors: Narumi Watanabe, Yuuto Ohnuki and Yasubumi Sakakibara
    Citation: Journal of Cheminformatics 2021 13:36
  7. Machine learning methods are widely used in drug discovery and toxicity prediction. While showing overall good performance in cross-validation studies, their predictive power (often) drops in cases where the q...

    Authors: Andrea Morger, Fredrik Svensson, Staffan Arvidsson McShane, Niharika Gauraha, Ulf Norinder, Ola Spjuth and Andrea Volkamer
    Citation: Journal of Cheminformatics 2021 13:35
  8. Chemical compounds can be identified through a graphical depiction, a suitable string representation, or a chemical name. A universally accepted naming scheme for chemistry was established by the International...

    Authors: Kohulan Rajan, Achim Zielesny and Christoph Steinbeck
    Citation: Journal of Cheminformatics 2021 13:34
  9. Despite being a central concept in cheminformatics, molecular similarity has so far been limited to the simultaneous comparison of only two molecules at a time and using one index, generally the Tanimoto coeff...

    Authors: Ramón Alain Miranda-Quintana, Anita Rácz, Dávid Bajusz and Károly Héberger
    Citation: Journal of Cheminformatics 2021 13:33
  10. Quantification of the similarity of objects is a key concept in many areas of computational science. This includes cheminformatics, where molecular similarity is usually quantified based on binary fingerprints...

    Authors: Ramón Alain Miranda-Quintana, Dávid Bajusz, Anita Rácz and Károly Héberger
    Citation: Journal of Cheminformatics 2021 13:32
  11. This article describes Flame, an open source software for building predictive models and supporting their use in production environments. Flame is a web application with a web-based graphic interface, which ca...

    Authors: Manuel Pastor, José Carlos Gómez-Tamayo and Ferran Sanz
    Citation: Journal of Cheminformatics 2021 13:31
  12. The assessment of protein–ligand interactions is critical at early stage of drug discovery. Computational approaches for efficiently predicting such interactions facilitate drug development. Recently, methods ...

    Authors: Fan Hu, Jiaxin Jiang, Dongqi Wang, Muchun Zhu and Peng Yin
    Citation: Journal of Cheminformatics 2021 13:30
  13. Quantitative structure activity relationships (QSAR) modelling is a well-known computational tool, often used in a wide variety of applications. Yet one of the major drawbacks of conventional QSAR modelling is...

    Authors: Amit Kumar Halder and M. Natália Dias Soeiro Cordeiro
    Citation: Journal of Cheminformatics 2021 13:29
  14. In drug discovery, rapid and accurate prediction of protein–ligand binding affinities is a pivotal task for lead optimization with acceptable on-target potency as well as pharmacological efficacy. Furthermore,...

    Authors: Surendra Kumar and Mi-hyun Kim
    Citation: Journal of Cheminformatics 2021 13:28
  15. A main challenge in drug discovery is finding molecules with a desirable balance of multiple properties. Here, we focus on the task of molecular optimization, where the goal is to optimize a given starting mol...

    Authors: Jiazhen He, Huifang You, Emil Sandström, Eva Nittinger, Esben Jannik Bjerrum, Christian Tyrchan, Werngard Czechtizky and Ola Engkvist
    Citation: Journal of Cheminformatics 2021 13:26
  16. The experimental values of skin permeability coefficients, required for dermal exposure assessment, are not readily available for many chemicals. The existing estimation approaches are either less accurate or ...

    Authors: Sana Naseem, Yasuyuki Zushi and Deedar Nabi
    Citation: Journal of Cheminformatics 2021 13:25
  17. Here, we introduce a new molecule optimization method, MolFinder, based on an efficient global optimization algorithm, the conformational space annealing algorithm, and the SMILES representation. MolFinder fin...

    Authors: Yongbeom Kwon and Juyong Lee
    Citation: Journal of Cheminformatics 2021 13:24
  18. Chemical data is increasingly openly available in databases such as PubChem, which contains approximately 110 million compound entries as of February 2021. With the availability of data at such scale, the burd...

    Authors: Janna Hastings, Martin Glauer, Adel Memariani, Fabian Neuhaus and Till Mossakowski
    Citation: Journal of Cheminformatics 2021 13:23
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
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