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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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