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Relevant bibliographies by topics / Pharmacophore generation

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Academic literature on the topic 'Pharmacophore generation'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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Journal articles on the topic "Pharmacophore generation"

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Mansi, Iman A., Mahmoud A. Al-Sha'er, Nizar M. Mhaidat, Mutasem O. Taha, and Rand Shahin. "Investigation of Binding Characteristics of Phosphoinositide-dependent Kinase-1 (PDK1) Co-crystallized Ligands Through Virtual Pharmacophore Modeling Leading to Novel Anti-PDK1 Hits." Medicinal Chemistry 16, no. 7 (2020): 860–80. http://dx.doi.org/10.2174/1573406415666190724131048.

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Background: 3-Phosphoinositide Dependent Protein Kinase-1 (PDK1) is being lately considered as an attractive and forthcoming anticancer target. A Protein Data Bank (PDB) cocrystallized crystal provides not only rigid theoretical data but also a realistic molecular recognition data that can be explored and used to discover new hits. Objective: This incited us to investigate the co-crystallized ligands' contacts inside the PDK1 binding pocket via a structure-based receptor-ligand pharmacophore generation technique in Discovery Studio 4.5 (DS 4.5). Methods: Accordingly, 35 crystals for PDK1 were

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Zhang, Yan Ling, Yuan Ming Wang, and Yan Jiang Qiao. "Sub-Pharmacophore Generation of JNK3 Inhibitors." Applied Mechanics and Materials 444-445 (October 2013): 1756–60. http://dx.doi.org/10.4028/www.scientific.net/amm.444-445.1756.

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The structure-based pharmacophore (SBP) model is consisted by the complementarity of the chemical features and space of the interaction between the ligand and receptor. The SBP models always have a high specificity which can only represent the specific class of the ligand. To simplify the models, sub-pharmacophore was then proposed in present study, and was expected to have and only have the most important or the common chemical features which play the major role in the interaction of ligand and receptor. Sub-pharmacophore should contain 4-6 features, the higher specificity with more features,

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Lu, Xin, Hongyu Yang, Yao Chen, et al. "The Development of Pharmacophore Modeling: Generation and Recent Applications in Drug Discovery." Current Pharmaceutical Design 24, no. 29 (2018): 3424–39. http://dx.doi.org/10.2174/1381612824666180810162944.

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Background: The pharmacophore concept in modern drug research is of great importance and promotes the development of drug industry as indicated by the number of publications available. Methods: : In this article, we reviewed and highlighted some successful examples of pharmacophore modeling, which was applied either in virtual screening for efficient hit discovery or in the optimization of the lead compounds. Meanwhile, the analysis of some important aspects of pharmacophore modeling such as a database, the software was listed as well. <p> Results: Based on the analysis of these examples

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Wang, Xing, Yanling Zhang, Yuhong Xiang, Zhenzhen Ren, and Yanjiang Qiao. "Pharmacophore Model Generation of Thrombin Inhibitors." Journal of Software Engineering and Applications 05, no. 12 (2012): 84–87. http://dx.doi.org/10.4236/jsea.2012.512b017.

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Van Drie, John H. "Generation of three-dimensional pharmacophore models." Wiley Interdisciplinary Reviews: Computational Molecular Science 3, no. 5 (2012): 449–64. http://dx.doi.org/10.1002/wcms.1129.

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Zhang, Yan Ling, Yuan Ming Wang, and Yan Jiang Qiao. "Structure-Based Pharmacophore Models Generation and Combinatorial Screening of ICE Inhibitors." Applied Mechanics and Materials 347-350 (August 2013): 1216–20. http://dx.doi.org/10.4028/www.scientific.net/amm.347-350.1216.

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Eight structure-based pharmacophore models of Interleukin-1β converting enzyme (ICE) inhibitors were generated by LigandScout based on ICE inhibitor complexes from the Protein Data Bank (PDB). A combinatorial screening method based on multiple pharmacophore models were proposed in present study, since the binding pockets of different complexes were different, the structure-based pharmacophore models have a high specificity and cannot cover all the active molecules. Based on the screening results of MDDR and the metrics of E and A%, a new metric CAI (comprehensive appraisal index) was defined a

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Sharma, Vidushi, Hirdesh Kumar, and Sharad Wakode. "Pharmacophore generation and atom based 3D-QSAR of quinoline derivatives as selective phosphodiesterase 4B inhibitors." RSC Advances 6, no. 79 (2016): 75805–19. http://dx.doi.org/10.1039/c6ra11210b.

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Reported PDE4B inhibitors were used to design QSAR based pharmacophore model. Using developed pharmacophore model, virtual screening was performed followed by cross-docking to identify novel PDE4B specific inhibitors.

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Gajjar, Krishna A., and Anuradha K. Gajjar. "Combiphore (Structure and Ligand Based Pharmacophore) - Approach for the Design of GPR40 Modulators in the Management of Diabetes." Current Drug Discovery Technologies 17, no. 2 (2020): 233–47. http://dx.doi.org/10.2174/1570163815666181008165822.

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Background: Pharmacophore mapping and molecular docking can be synergistically integrated to improve the drug design and discovery process. A rational strategy, combiphore approach, derived from the combined study of Structure and Ligand based pharmacophore has been described to identify novel GPR40 modulators. Methods: DISCOtech module from Discovery studio was used for the generation of the Structure and Ligand based pharmacophore models which gave hydrophobic aromatic, ring aromatic and negative ionizable as essential pharmacophoric features. The generated models were validated by screening

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Patel, Vijay K., and Harish Rajak. "Development of Structure Activity Correlation Model on Aroylindole Derivatives as Anticancer Agents." Letters in Drug Design & Discovery 15, no. 2 (2018): 143–53. http://dx.doi.org/10.2174/1570180814666170823161751.

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Background: Aroylindole derivatives, the structural analogs of Combretastatin A-4 has been found to possess potent growth inhibitory activity on several cancer cell lines due to its excellent antitumor and antivascular activities. The aim of present research work is to identify lead and establish structure activity correlation of trimethoxyaroylindole derivatives, using integrated ligand and structure based computational approaches. Materials and Methods: A correlation between structure and biological activity was established using computational approaches i.e., structure activity correlation

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Hong-Juan, BAO, ZHANG Yan-Ling, and QIAO Yan-Jiang. "Pharmacophore Model Generation of HMG-CoA Reductase Inhibitors." Acta Physico-Chimica Sinica 24, no. 02 (2008): 301–6. http://dx.doi.org/10.3866/pku.whxb20080220.

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Dissertations / Theses on the topic "Pharmacophore generation"

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Cottrell, Simon John. "Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques." Thesis, University of Sheffield, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.422173.

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Su, Li. "Generation of analogues of the anti-tumor polyketide stambomycins by genetic engineering and allied approaches." Electronic Thesis or Diss., Université de Lorraine, 2021. http://www.theses.fr/2021LORR0081.

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Les polycétides d’origine bactérienne sont une source importante de molécules anti-infectieuses et anticancéreuses d’origine naturelle utilisées en thérapie. Cependant, leurs structures doivent souvent être optimisées afin d'améliorer leurs propriétés thérapeutiques. Les stambomycines, une famille de macrolides parmi les plus grands polycétides connus (elles possèdent un noyau macrolactone à 51 membres), ont été récemment découvertes par une approche de genome mining chez la bactérie Streptomyces ambofaciens ATCC23877. Ces molécules présentent une activité anticancéreuse prometteuse. Six forme

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Lu, Chien-Sheng, and 盧建勝. "Study on Generation of Chemical Function Based Pharmacophore Models for Hepatitis C virus NS3 Protease Inhibitors." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/7kx8mz.

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碩士<br>國立清華大學<br>分子醫學研究所<br>92<br>Chmical function based pharmacophore models were developed for a series of pyrimidinone- and pyrazinone-based HCV NS3 protease inhibitors. The pharmacophore models were generated using a training set consisting of 20 inhibitors. The activity spread, expressed in IC50 of training set molecules was from 20 to 30000 nM. The most predictive pharmacophore model (hypothesis 1), consisting of three features, namely, two hydrophobic, one hydrogen bond donor and one hydrophobic aromatic, had a correlation (r) of 0.943 and a root mean square of 0.886, and the cost differ

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Chiang, Yi-Kun, and 姜義坤. "Generation of Ligand-Based Pharmacophore Model and Virtual Screening for Identification of Novel Tubulin Inhibitors with Potent Cellular Anticancer Activity." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/96192529700177694426.

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碩士<br>國立清華大學<br>生物資訊與結構生物研究所<br>97<br>A pharmacophore model, Hypo1, was built based on 21 training-set indole compounds with varying levels of antiproliferative activity. Hypo1 possessed important chemical features required for the inhibitors and demonstrated good predictive ability for biological activity with high correlation coefficient of 0.96 and 0.89 for the training-set and test-set compounds, respectively. Further utilization of Hypo1 pharmacophore model to screen chemical database in silico led to the identification of four compounds with antiproliferative activity. Among these four c

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Meduru, Harika, and Harika Meduru. "Dipeptidyl Peptidase-4 (DPP-4) Enzyme Inhibitor Study by In Silico Analysis: Molecular Docking, Pharmacophore Generation and Molecular Dynamics Simulation in Treatment of Type-2 Diabetes." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/55336938559078403490.

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博士<br>亞洲大學<br>生物資訊與醫學工程學系<br>104<br>Dipeptidyl peptidase-4 (DPP-4) is the vital enzyme responsible for inactivating intestinal peptides Glucagon like peptide-1 (GLP-1) and Gastric inhibitory polypeptide (GIP), which stimulates a decrease in blood glucose levels. The aim of this study was to explore the inhibition activity of small-molecule inhibitors to DPP-4. AutoDock, CDOCKER and Standard dynamics cascade were used for molecular docking and molecular dynamics studies. Molecular docking was performed for structurally diverse compounds (Aminopiperdine-fused imidazoles, Thiazolopyrimidine deriv

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Thullen, Scott Macmillan. "Novel Methodologies for the Photochemical and Photocatalytic Generation of Nitrogen-Containing Pharmacophores." Thesis, 2018. https://doi.org/10.7916/D8DN5NM4.

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Photochemical transformations give rise to radical intermediates that are enabling tools for constructing molecular scaffolds in alternative methods from traditional two-electron processes. Herein, we detail four discrete projects focused on harnessing photochemically-created radicals for building nitrogen-containing architectures. We first explored a formal [5+2] photochemical cycloaddition of vinyl-pyrrolidinones in order to efficiently reach densely functionalized azepane motifs from simple aldehydes and pyrrolidinones. Second, we describe the discovery and development of a cobalt and photo

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Books on the topic "Pharmacophore generation"

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Thullen, Scott Macmillan. Novel Methodologies for the Photochemical and Photocatalytic Generation of Nitrogen-Containing Pharmacophores. [publisher not identified], 2018.

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Zaheer Ul-Haq and Angela K. Wilson, eds. Frontiers in Computational Chemistry: Volume 6. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150368481220601.

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Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug development process: computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity. The sixth volume of this series features these six different perspectives on the application of computational chemistry in rationa

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Book chapters on the topic "Pharmacophore generation"

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Hoksza, David, and Petr Škoda. "2D Pharmacophore Query Generation." In Bioinformatics Research and Applications. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-08171-7_26.

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Handler, Norbert. "Pharmacophore Generation for Multiple Ligands." In Methods and Principles in Medicinal Chemistry. Wiley-VCH Verlag GmbH & Co. KGaA, 2017. http://dx.doi.org/10.1002/9783527674381.ch10.

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Vrontaki, Eleni, and Antonios Kolocouris. "Pharmacophore Generation and 3D-QSAR Model Development Using PHASE." In Methods in Molecular Biology. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8630-9_23.

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Pathak, Dharmraj V., Abha Vyas, Hardik G. Bhatt, and Paresh K. Patel. "Pharmacophore Mapping: An Important Tool in Modern Drug Design and Discovery." In Applied Computer-Aided Drug Design: Models and Methods. BENTHAM SCIENCE PUBLISHERS, 2023. http://dx.doi.org/10.2174/9789815179934123010005.

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Computer-Aided Drug Design (CADD) has become an integral part of drug discovery and development efforts in the pharmaceutical and biotechnology industry. Since the 1980s, structure-based design technology has evolved, and today, these techniques are being widely employed and credited for the discovery and design of most of the recent drug products in the market. Pharmacophore-based drug design provides fundamental approach strategies for both structure-based and ligand-based pharmacophore approaches. The different programs and methodologies enable the implementation of more accurate and sophis

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Conference papers on the topic "Pharmacophore generation"

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Yang, Zhen, Yanling Zhang, Xing Wang, and Yanjiang Qiao. "Pharmacophore Model Generation of P2Y12 Inhibitor." In 2012 International Conference on Biomedical Engineering and Biotechnology (iCBEB). IEEE, 2012. http://dx.doi.org/10.1109/icbeb.2012.293.

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Zhang, Yanling, Yuanming Wang, and Yanjiang Qiao. "Structure-based pharmacophore models generation and Combinatorial Screening of ICE Inhibitors." In 2nd International Symposium on Computer, Communication, Control and Automation. Atlantis Press, 2013. http://dx.doi.org/10.2991/isccca.2013.110.

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DUBE, PRITAM, SANTOSH MOKALE, and VIVEKANAND CHATPALLIWAR. "Insight into the structural requirement for Anticancer Activity: Pharmacophore Generation and 3D QSAR Analysis ." In The 19th International Electronic Conference on Synthetic Organic Chemistry. MDPI, 2015. http://dx.doi.org/10.3390/ecsoc-19-e004.

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Alargić, Aleksa P., Bojan D. Levovnik, and Miloš M. Svirčev. "Workflow automation of high-throughput inverse docking using Pharmmapper." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.678a.

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In this paper, we present a novel, modular script Pharmmapper-Mass-Docker for the inverse docking workflow automation based on the pharmacophore screening results obtained on the Pharmmapper server. Pharmmapper-Mass-Docker streamlines download, manipulation, and entire inverse docking of the Pharmmapper results, encompassing essential steps like ligand/gridbox/binding site coordinate extraction (via centroid generation) and obtaining the output data ready for further comprehensive data analysis. By automating the entire inverse docking procedure, our modular script potentially enhances data ma

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Hossain, Kazi Amirul. "Generating optimal features to find out potent molecules against dengue virus: pharmacophore and QSAR approaches." In MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition. MDPI, 2018. http://dx.doi.org/10.3390/mol2net-04-05908.

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Hossain, Kazi Amirul. "Generating optimal features to find out potent molecules against dengue virus: pharmacophore and QSAR approaches." In MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition. MDPI, 2018. http://dx.doi.org/10.3390/mol2net-04-05907.

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Zhang, Yanling, Yuanming Wang, and Yanjiang Qiao. "Pharmacophores generation of multiple anti-inflammatory targets and identification of active compounds in Chinese herbs." In 2013 7th International Conference on Systems Biology (ISB). IEEE, 2013. http://dx.doi.org/10.1109/isb.2013.6623787.

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