Skip to main content

Articles

373 result(s) for 'PubChem' within Journal of Cheminformatics

Page 3 of 8

  1. Here we present DRABAL, a novel MLC solution that incorporates structure learning of a Bayesian network as a step to model dependency between the HTS assays. In this study, DRABAL was used to process more than 1....

    Authors: Othman Soufan, Wail Ba-Alawi, Moataz Afeef, Magbubah Essack, Panos Kalnis and Vladimir B. Bajic
    Citation: Journal of Cheminformatics 2016 8:64
  2. The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failur...

    Authors: Ashenafi Legehar, Henri Xhaard and Leo Ghemtio
    Citation: Journal of Cheminformatics 2016 8:33
  3. The Java application cApp addresses this need and aids in the handling and storage of information on small-molecule compounds. The software is intended for the appraisal of compounds with respect to their physico...

    Authors: Parisa Amani, Todd Sneyd, Sarah Preston, Neil D Young, Lyndel Mason, Ulla-Maja Bailey, Jonathan Baell, David Camp, Robin B Gasser, Alain-Dominique Gorse, Paul Taylor and Andreas Hofmann
    Citation: Journal of Cheminformatics 2015 7:28
  4. Skin sensitization is an important toxicological endpoint for chemical hazard determination and safety assessment. Prediction of chemical skin sensitizer had traditionally relied on data from rodent models. Th...

    Authors: Chia-Chi Wang, Ying-Chi Lin, Shan-Shan Wang, Chieh Shih, Yi-Hui Lin and Chun-Wei Tung
    Citation: Journal of Cheminformatics 2017 9:5
  5. Several QSAR methodology developments have shown promise in recent years. These include the consensus approach to generate the final prediction of a model, utilizing new, advanced machine learning algorithms a...

    Authors: Kristijan Vukovic, Domenico Gadaleta and Emilio Benfenati
    Citation: Journal of Cheminformatics 2019 11:27
  6. MicroRNAs (miRNA) are small endogenously transcribed regulatory RNA which modulates gene expression at a post transcriptional level. These small RNAs have now been shown to be critical regulators in a number o...

    Authors: Salma Jamal, Vinita Periwal, OpenSourceDrugDiscovery Consortium and Vinod Scaria
    Citation: Journal of Cheminformatics 2012 4:16
  7. High throughput screening (HTS) is widely used in drug discovery and chemical biology to identify and characterize agents having pharmacologic properties often by evaluation of large chemical libraries. Standa...

    Authors: Bryan Queme, John C. Braisted, Patricia Dranchak and James Inglese
    Citation: Journal of Cheminformatics 2023 15:39
  8. A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editor...

    Authors: Peter Ertl
    Citation: Journal of Cheminformatics 2010 2:1
  9. Methods that provide a measure of chemical similarity are strongly relevant in several fields of chemoinformatics as they allow to predict the molecular behavior and fate of structurally close compounds. One c...

    Authors: Matteo Floris, Alberto Manganaro, Orazio Nicolotti, Ricardo Medda, Giuseppe Felice Mangiatordi and Emilio Benfenati
    Citation: Journal of Cheminformatics 2014 6:39
  10. Application of chemical named entity recognition (CNER) algorithms allows retrieval of information from texts about chemical compound identifiers and creates associations with physical–chemical properties and ...

    Authors: O. A. Tarasova, A. V. Rudik, N. Yu. Biziukova, D. A. Filimonov and V. V. Poroikov
    Citation: Journal of Cheminformatics 2022 14:55
  11. The Chemistry Development Kit (CDK) is an open source Java library for manipulating and processing chemical information. A key aspect in handling chemical structures is the determination of the chemical rings....

    Authors: John W May and Christoph Steinbeck
    Citation: Journal of Cheminformatics 2014 6:3
  12. Measurements of protein–ligand interactions have reproducibility limits due to experimental errors. Any model based on such assays will consequentially have such unavoidable errors influencing their performanc...

    Authors: Lewis H. Mervin, Maria-Anna Trapotsi, Avid M. Afzal, Ian P. Barrett, Andreas Bender and Ola Engkvist
    Citation: Journal of Cheminformatics 2021 13:62
  13. This article contains the slides and transcript of a talk given by Dan Zaharevitz at the "Visions of a Semantic Molecular Future" symposium held at the University of Cambridge Department of Chemistry on 2011-0...

    Authors: Dan W Zaharevitz
    Citation: Journal of Cheminformatics 2011 3:34
  14. 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
  15. Natural products from traditional medicine inherit bioactivity from their source herbs. However, the pharmacological mechanism of natural products is often unclear and studied insufficiently. Pathway fingerpri...

    Authors: Feifei Guo, Chunhong Jiang, Yujie Xi, Dan Wang, Yi Zhang, Ning Xie, Yi Guan, Fangbo Zhang and Hongjun Yang
    Citation: Journal of Cheminformatics 2021 13:68
  16. REINVENT 4 is a modern open-source generative AI framework for the design of small molecules. The software utilizes recurrent neural networks and transformer architectures to drive molecule generation. These g...

    Authors: Hannes H. Loeffler, Jiazhen He, Alessandro Tibo, Jon Paul Janet, Alexey Voronov, Lewis H. Mervin and Ola Engkvist
    Citation: Journal of Cheminformatics 2024 16:20
  17. Homologous series are groups of related compounds that share the same core structure attached to a motif that repeats to different degrees. Compounds forming homologous series are of interest in multiple domai...

    Authors: Adelene Lai, Jonas Schaub, Christoph Steinbeck and Emma L. Schymanski
    Citation: Journal of Cheminformatics 2022 14:85
  18. Facing the continuous emergence of new psychoactive substances (NPS) and their threat to public health, more effective methods for NPS prediction and identification are critical. In this study, the pharmacolog...

    Authors: Kedan He
    Citation: Journal of Cheminformatics 2022 14:35

    The Correction to this article has been published in Journal of Cheminformatics 2022 14:42

  19. The ability to access chemical information openly is an essential part of many scientific disciplines. The Journal of Cheminformatics is leading the way for rigorous, open cheminformatics in many ways, but the...

    Authors: Emma L. Schymanski and Evan E. Bolton
    Citation: Journal of Cheminformatics 2021 13:50

    The Letter Response to this article has been published in Journal of Cheminformatics 2021 13:49

  20. Drug discovery investigations need to incorporate network pharmacology concepts while navigating the complex landscape of drug-target and target-target interactions. This task requires solutions that integrate...

    Authors: Gergely Zahoránszky-Kőhalmi, Timothy Sheils and Tudor I. Oprea
    Citation: Journal of Cheminformatics 2020 12:5
  21. The median lethal dose for rodent oral acute toxicity (LD50) is a standard piece of information required to categorize chemicals in terms of the potential hazard posed to human health after acute exposure. The...

    Authors: Domenico Gadaleta, Kristijan Vuković, Cosimo Toma, Giovanna J. Lavado, Agnes L. Karmaus, Kamel Mansouri, Nicole C. Kleinstreuer, Emilio Benfenati and Alessandra Roncaglioni
    Citation: Journal of Cheminformatics 2019 11:58
  22. Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a s...

    Authors: Mathilde Koch, Thomas Duigou, Pablo Carbonell and Jean-Loup Faulon
    Citation: Journal of Cheminformatics 2017 9:64
  23. In ligand-based virtual screening experiments, a known active ligand is used in similarity searches to find putative active compounds for the same protein target. When there are several known active molecules,...

    Authors: Francois Berenger, Oanh Vu and Jens Meiler
    Citation: Journal of Cheminformatics 2017 9:60
  24. Despite the increasing knowledge in both the chemical and biological domains the assimilation and exploration of heterogeneous datasets, encoding information about the chemical, bioactivity and phenotypic prop...

    Authors: Chad H. G. Allen, Lewis H. Mervin, Samar Y. Mahmoud and Andreas Bender
    Citation: Journal of Cheminformatics 2019 11:36
  25. The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern sol...

    Authors: Pierre Tremouilhac, An Nguyen, Yu-Chieh Huang, Serhii Kotov, Dominic Sebastian Lütjohann, Florian Hübsch, Nicole Jung and Stefan Bräse
    Citation: Journal of Cheminformatics 2017 9:54
  26. NPCARE (http://​silver.​sejong.​ac.​kr/​npcare...) is a publicly accessible online database of natural products and fractional extracts for cancer regulatio...

    Authors: Hwanho Choi, Sun Young Cho, Ho Jeong Pak, Youngsoo Kim, Jung-yun Choi, Yoon Jae Lee, Byung Hee Gong, Yeon Seok Kang, Taehoon Han, Geunbae Choi, Yeeun Cho, Soomin Lee, Dekwoo Ryoo and Hwangseo Park
    Citation: Journal of Cheminformatics 2017 9:2
  27. Wikipedia, the world’s largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, a...

    Authors: Peter Ertl, Luc Patiny, Thomas Sander, Christian Rufener and Michaël Zasso
    Citation: Journal of Cheminformatics 2015 7:10
  28. Plants are one of the primary sources of natural products for drug development. However, despite centuries of research, only a limited region of the phytochemical space has been studied. To understand the scop...

    Authors: Daniel Domingo-Fernández, Yojana Gadiya, Sarah Mubeen, David Healey, Bryan H. Norman and Viswa Colluru
    Citation: Journal of Cheminformatics 2023 15:107
  29. We collected data from over 80 different cytotoxicity assays from Pfizer in-house work as well as from public sources and investigated the feasibility of using these datasets, which come from a variety of assa...

    Authors: Sarah R Langdon, Joanna Mulgrew, Gaia V Paolini and Willem P van Hoorn
    Citation: Journal of Cheminformatics 2010 2:11
  30. The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from...

    Authors: Kerstin Scheubert, Franziska Hufsky and Sebastian Böcker
    Citation: Journal of Cheminformatics 2013 5:12
  31. Tuberculosis (TB) is the second leading cause of death from a single infectious organism, demanding attention towards discovery of novel anti-tubercular compounds. Natural products or their derivatives have pr...

    Authors: Arun Sharma, Prasun Dutta, Maneesh Sharma, Neeraj Kumar Rajput, Bhavna Dodiya, John J Georrge, Trupti Kholia and Anshu Bhardwaj
    Citation: Journal of Cheminformatics 2014 6:46
  32. OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical...

    Authors: Barry Hardy, Nicki Douglas, Christoph Helma, Micha Rautenberg, Nina Jeliazkova, Vedrin Jeliazkov, Ivelina Nikolova, Romualdo Benigni, Olga Tcheremenskaia, Stefan Kramer, Tobias Girschick, Fabian Buchwald, Joerg Wicker, Andreas Karwath, Martin Gütlein, Andreas Maunz…
    Citation: Journal of Cheminformatics 2010 2:7
  33. The discovery and utilization of natural products derived from endophytic microorganisms have garnered significant attention in pharmaceutical research. While remarkable progress has been made in this field ea...

    Authors: Hong-Quan Xu, Huan Xiao, Jin-Hui Bu, Yan-Feng Hong, Yu-Hong Liu, Zi-Yue Tao, Shu-Fan Ding, Yi-Tong Xia, E Wu, Zhen Yan, Wei Zhang, Gong-Xing Chen, Feng Zhu and Lin Tao
    Citation: Journal of Cheminformatics 2023 15:115
  34. Modern computer-assisted synthesis planning tools provide strong support for this problem. However, they are still limited by computational complexity. This limitation may be overcome by scoring the synthetic ...

    Authors: Grzegorz Skoraczyński, Mateusz Kitlas, Błażej Miasojedow and Anna Gambin
    Citation: Journal of Cheminformatics 2023 15:6
  35. Drug–drug interaction (DDI) often causes serious adverse reactions and thus results in inestimable economic and social loss. Currently, comprehensive DDI evaluation has become a major challenge in pharmaceutic...

    Authors: Ning-Ning Wang, Xiang-Gui Wang, Guo-Li Xiong, Zi-Yi Yang, Ai-Ping Lu, Xiang Chen, Shao Liu, Ting-Jun Hou and Dong-Sheng Cao
    Citation: Journal of Cheminformatics 2022 14:23
  36. 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
  37. The reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilizat...

    Authors: Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth and Chanin Nantasenamat
    Citation: Journal of Cheminformatics 2020 12:9