Relevant bibliographies by topics / PHARMACOPHORE MODELING

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'PHARMACOPHORE MODELING'

Author: Grafiati
Published: 11 September 2023
Last updated: 25 July 2025

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Journal articles on the topic "PHARMACOPHORE MODELING"

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Kutlushina, Alina, Aigul Khakimova, Timur Madzhidov, and Pavel Polishchuk. "Ligand-Based Pharmacophore Modeling Using Novel 3D Pharmacophore Signatures." Molecules 23, no. 12 (2018): 3094. http://dx.doi.org/10.3390/molecules23123094.

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Pharmacophore modeling is a widely used strategy for finding new hit molecules. Since not all protein targets have available 3D structures, ligand-based approaches are still useful. Currently, there are just a few free ligand-based pharmacophore modeling tools, and these have a lot of restrictions, e.g., using a template molecule for alignment. We developed a new approach to 3D pharmacophore representation and matching which does not require pharmacophore alignment. This representation can be used to quickly find identical pharmacophores in a given set. Based on this representation, a 3D pharm
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Mortier, Jérémie, Pratik Dhakal, and Andrea Volkamer. "Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces." Molecules 23, no. 8 (2018): 1959. http://dx.doi.org/10.3390/molecules23081959.

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Pharmacophore models are an accurate and minimal tridimensional abstraction of intermolecular interactions between chemical structures, usually derived from a group of molecules or from a ligand-target complex. Only a limited amount of solutions exists to model comprehensive pharmacophores using the information of a particular target structure without knowledge of any binding ligand. In this work, an automated and customable tool for truly target-focused (T²F) pharmacophore modeling is introduced. Key molecular interaction fields of a macromolecular structure are calculated using the AutoGRID
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Madzhidov, Timur I., Assima Rakhimbekova, Alina Kutlushuna, and Pavel Polishchuk. "Probabilistic Approach for Virtual Screening Based on Multiple Pharmacophores." Molecules 25, no. 2 (2020): 385. http://dx.doi.org/10.3390/molecules25020385.

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Pharmacophore modeling is usually considered as a special type of virtual screening without probabilistic nature. Correspondence of at least one conformation of a molecule to pharmacophore is considered as evidence of its bioactivity. We show that pharmacophores can be treated as one-class machine learning models, and the probability the reflecting model’s confidence can be assigned to a pharmacophore on the basis of their precision of active compounds identification on a calibration set. Two schemes (Max and Mean) of probability calculation for consensus prediction based on individual pharmac
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Kumar, Saurav, Deepika Deepika, and Vikas Kumar. "Pharmacophore Modeling Using Machine Learning for Screening the Blood–Brain Barrier Permeation of Xenobiotics." International Journal of Environmental Research and Public Health 19, no. 20 (2022): 13471. http://dx.doi.org/10.3390/ijerph192013471.

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Daily exposure to xenobiotics affects human health, especially the nervous system, causing neurodegenerative diseases. The nervous system is protected by tight junctions present at the blood–brain barrier (BBB), but only molecules with desirable physicochemical properties can permeate it. This is why permeation is a decisive step in avoiding unwanted brain toxicity and also in developing neuronal drugs. In silico methods are being implemented as an initial step to reduce animal testing and the time complexity of the in vitro screening process. However, most in silico methods are ligand based,
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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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AFFI, Sopi Thomas, Doh SORO, Souleymane COULIBALY, Bibata KONATE, and Nahossé ZIAO. "Modeling anticancer pharmacophore based on inhibition of HDAC7." SDRP Journal of Computational Chemistry & Molecular Modeling 5, no. 3 (2021): 657–63. http://dx.doi.org/10.25177/jccmm.5.3.ra.10776.

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Histone deacetylases (HDACs) are the target inhibition enzymes in cancer treatment via chemotherapy. Application of this therapeutic technique requires the use of drugs whose side effects are reduced and tiny with necessary safety. In this study, the methods and tools of pharmacophore modeling were used to investigate ten molecules known for their anticancer properties. Particular attention has been given to pinpoint a promising anti-cancer pharmacophore in order to lead new effective inhibitors. Using Discovery Studio 2.5 software, the ten compounds were docked within the active site of the H
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Kadu, Nilesh S., and Atul V. Ingle. "Three-Dimensional Pharmacophore Modeling of Betulonic Acid Derivatives as a Strong Inhibitor of Human Coronavirus-229E Replication." International Journal of Science and Healthcare Research 6, no. 2 (2021): 356–61. http://dx.doi.org/10.52403/ijshr.20210462.

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These-days, pharmacophore approaches have become one of the foremost tools in drug discovery after the past century’s development. Numerous ligand-based and structure-based strategies are developed for improved pharmacophore modeling with success and extensively applied in virtual screening, de novo design and lead improvement. Till now, there is little information on 3D-pharmacophore studies of 1,2,3-triazolo-fused betulonic acid derivatives as a strong inhibitor for human coronavirus-229E replication. Here, we tend to report the appliance of pharmacophore modeling for betulonic acid derivati
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Mendez, Nixon, and Md Afroz Alam. "Structural Features of Quercetin Derivatives by Using Pharmaco-phore Modeling Approach." Open Pharmaceutical Sciences Journal 3, no. 1 (2016): 79–98. http://dx.doi.org/10.2174/1874844901603010079.

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Background:Quercetin which is a natural occurring flavonoid, exert a direct pro-apoptotic effect on tumor cells by blocking the growth of several cancer cell lines at different phases of the cell cycle. Quercetin derivatives have attracted considerable attention for their cytotoxity against human cancer cell lines. In this study the derivatives of Quercetin were used for docking followed by pharmacophore modeling for studying the 3D features and configurations responsible for biological activity of structurally diverse compounds.Objective:To develop a model which depicts the crucial structural
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Vaddavalli, Radha, Bagyanaryana Gaddam, and Pradeep Kumar Maddikara. "Discovery of Novel Inhibitors Against Resistant Streptococcus pneumoniae MurF Enzyme using Phamracophore Modeling and QSAR Analysis." International Journal of Drug Design and Discovery 2, no. 1 (2024): 403–12. https://doi.org/10.37285/ijddd.2.1.7.

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Main aim of the current study was to discover novel inhibitors against Streptococcus pneumoniae MurF enzyme using analogue based drug design. Pharmacophore mapping and 3D-QSAR analysis was performed on some previously synthesized and evaluated sulfonamide derivatives which are known to be potent inhibitors of penicillin resistant Streptococcus pneumoniae MurF receptor. 3D-QSAR study based on the principle of alignment of pharmacophoric features was performed on the same set of inhibitors using the PHASE module of Schrodinger suite. A five point pharmacophore, ADHRR, with one hydrogen bond acce
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Thai, Khac-Minh, Trieu-Du Ngo, Thanh-Dao Tran, and Minh-Tri Le. "Pharmacophore Modeling for Antitargets." Current Topics in Medicinal Chemistry 13, no. 9 (2013): 1002–14. http://dx.doi.org/10.2174/1568026611313090004.

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Dissertations / Theses on the topic "PHARMACOPHORE MODELING"

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Vendruscolo, Maria Helena. "Obtenção de iridoides de espécies nativas da flora do Rio Grande do Sul, modificações estruturais, determinação da atividade anti-Leishmania amazonensis in vitro e modelagem molecular." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2017. http://hdl.handle.net/10183/166272.

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Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo comumente na forma glicosilada. Estes compostos são marcadores taxonômicos em algumas famílias vegetais e apresentam diversas atividades biológicas tais como cardiovascular, neuroprotetora e anti-Leishmania. Diante da importância dos iridoides, este trabalho teve como finalidade a prospecção química destes metabólitos em espécies nativas do Rio Grande Grande dos Sul, bem
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Argade, Malaika. "Galantamine's Deconstruction in the Quest of a PAM Pharmacophore." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5461.

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Alzheimer’s disease is a progressive neurodegenerative disorder generally affecting people above the age of 65 years. Even though the pathophysiological hallmarks of AD were established more than a hundred years ago, there is yet to be a drug that can stop its characteristic neuronal damage. Of the five currently FDA-approved drugs, galantamine has a unique mechanism of action. Apart from being an AChE inhibitor, galantamine can effectively potentiate (positive allosteric modulator) the effect of agonists at nAChRs at concentrations lower than those required for its action as an AChE inhibitor
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Aldhumani, Ali Hamed. "Pharmacophore Model Development: Targeting Noncoding RNA for Antibacterial/Antiviral Drug Discovery." Ohio University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1610705872573225.

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Varela, Rial Alejandro 1993. "In silico modeling of protein-ligand binding." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2022. http://hdl.handle.net/10803/673579.

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The affinity of a drug to its target protein is one of the key properties of a drug. Although there are experimental methods to measure the binding affinity, they are expensive and relatively slow. Hence, accurately predicting this property with software tools would be very beneficial to drug discovery. In this thesis, several applications have been developed to model and predict the binding mode of a ligand to a protein, to evaluate the feasibility of that prediction and to perform model interpretability in deep neural networks trained on protein-ligand complexes.<br>La afinidad de un fármaco
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Chang, Cheng. "In silico approaches for studying transporter and receptor structure-activity relationships." Connect to this title online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1117553995.

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Thesis (Ph. D.)--Ohio State University, 2005.<br>Title from first page of PDF file. Document formatted into pages; contains xvii, 271 p.; also includes graphics. Includes bibliographical references (p. 245-269). Available online via OhioLINK's ETD Center
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Shah, Urjita H. "A Roadmap for Development of Novel Antipsychotic Agents Based on a Risperidone Scaffold." VCU Scholars Compass, 2017. http://scholarscompass.vcu.edu/etd/4804.

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Schizophrenia is a chronic psychotic illness affecting ~21 million people globally. Currently available antipsychotic agents act through a dopamine D2 receptor mechanism, and produce extrapyramidal or metabolic side effects. Hence, there is a need for novel targets and agents. The mGlu2/5-HT2A receptor heteromer has been implicated in the action of antipsychotic agents, and represents a novel and attractive therapeutic target for the treatment of schizophrenia. A long-term goal of this project is to synthesize bivalent ligands where a 5-HT2A receptor antagonist is tethered to an mGlu2 PAM via
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Klenc, Jeffrey D. "Design and Synthesis of Novel Serotonin Receptor Ligands." Digital Archive @ GSU, 2010. http://digitalarchive.gsu.edu/chemistry_diss/50.

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Novel and potent ligands to the serotonin7 (5-HT7) receptor have been synthesized. The synthesized compounds include a set of substituted pyrimidines which show high affinity to the 5-HT7 receptor, synthesized by previously described methods [1,2] in high yield. Comparing the affinities of substituted pyrimidines to previously calculated models [3,4] yielded new hypotheses about the nature of interaction between the pyrimidine ligands and the 5-HT7 binding site. Several new series of compounds were synthesized by various methods to validate these hypotheses, including a conjugate addition t
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Wong, Carmen Ka-Wing. "Unlocking mechanisms implicated in drug-induced bizarre idiosyncratic behaviours - learning from people and molecules." Thesis, The University of Sydney, 2016. http://hdl.handle.net/2123/16263.

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Zolpidem, an imidazopyridine hypnotic, which acts on GABA‐A receptors has been associated with the development of a number of disturbing neuropsychiatric adverse drug reactions (ADRs) including parasomnias, amnesia and hallucinations. Although other non-hypnotic medications are also implicated in the induction of such adverse events; the mechanism behind these ADRs remains elusive and have been postulated to arise from off-target receptor or pathway activation resulting in the disruption and dysregulation of keyneurotransmitters including GABA, acetylcholine, noradrenaline and dopamine. Using
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Afzelius, Lovisa. "Computational Modelling of Structures and Ligands of CYP2C9." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4016.

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Junior, Nilson Nicolau. "Diferenças Estruturais e \"Docking\" Receptor-Ligante da Proteína E7 do Vírus do Papiloma Humano (HPV) de Alto e Baixo Riscos para o Câncer Cervical." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-13062013-092311/.

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O câncer cervical afeta milhões de mulheres em todo o mundo a cada ano. A maioria dos casos de câncer cervical é causada pelo vírus do papiloma humano (HPV) que é sexualmente transmissível. Cerca de 40 tipos de HPV infectam o colo do útero e estes são designados como sendo de alto ou de baixo risco com base no seu potencial para provocar lesões de alto grau e câncer. A oncoproteína E7 do HPV está diretamente envolvida no aparecimento de câncer de colo do útero. Esta se associada com a proteína pRb e outros alvos celulares que promovem a imortalização celular e carcinogênese. Apesar de muito pr
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Books on the topic "PHARMACOPHORE MODELING"

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Beneditti, P. G. De. Theoretical Approaches to Quantitative Pharmacophore Modeling Biological Activity Relationships (Tcc , Vol 7). Elsevier Science Ltd, 1998.

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Thakur, Aman, Vineet Mehta, Priyanka Nagu, and Kiran Goutam. Computer-Aided Drug Design: QSAR, Molecular Docking, Virtual Screening, Homology and Pharmacophore Modeling. de Gruyter GmbH, Walter, 2024.

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Thakur, Aman, Vineet Mehta, Priyanka Nagu, and Kiran Goutam. Computer-Aided Drug Design: QSAR, Molecular Docking, Virtual Screening, Homology and Pharmacophore Modeling. de Gruyter GmbH, Walter, 2024.

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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 MODELING"

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Koes, David Ryan. "Pharmacophore Modeling: Methods and Applications." In Methods in Pharmacology and Toxicology. Springer New York, 2015. http://dx.doi.org/10.1007/7653_2015_46.

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Dharkiya, Sandhya, Rukayya, and Sisir Nandi. "Pharmacophore Modeling of Tricyclic Antipsychotics." In Global Trends in Health, Technology and Management. Springer Nature Switzerland, 2024. https://doi.org/10.1007/978-3-031-75457-9_19.

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Takahashi, Mitsuo, Kuniya Sakurai, Seji Niwa, and Seiji Oono. "Pharmacophore Model of Endothelin Antagonists." In Molecular Modeling and Prediction of Bioactivity. Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4141-7_103.

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Bhattacharjee, Apurba K. "Pharmacophore Modeling Applied to Mosquito-Borne Diseases." In Computational Design of Chemicals for the Control of Mosquitoes and Their Diseases. CRC Press, 2017. http://dx.doi.org/10.4324/9781315151656-5.

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Froloff, Nicolas. "Pharmacophore Modeling of Sweet and Bitter Tasting Molecules." In Sweetness and Sweeteners. American Chemical Society, 2008. http://dx.doi.org/10.1021/bk-2008-0979.ch009.

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Boström, Jonas, Klaus Gundertofte, and Tommy Liljefors. "A 3D-Pharmacophore Model for Dopamine D4 Receptor Antagonists." In Molecular Modeling and Prediction of Bioactivity. Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4141-7_87.

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Høst, Jan, Inge Thøger Christensen, and Flemming Steen Jørgensen. "Conformational Analysis and Pharmacophore Identification of Potential Drugs for Osteoporosis." In Molecular Modeling and Prediction of Bioactivity. Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4141-7_83.

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Swaminathan, Priya. "Advances in Pharmacophore Modeling and Its Role in Drug Designing." In Computer-Aided Drug Design. Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-6815-2_10.

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Seidel, Thomas, Sharon D. Bryant, Gökhan Ibis, Giulio Poli, and Thierry Langer. "3D Pharmacophore Modeling Techniques in Computer-Aided Molecular Design Using LigandScout." In Tutorials in Chemoinformatics. John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781119161110.ch20.

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Kumar, Pawan, and Indira Ghosh. "Probing with Pharmacophore Modeling the Chloroquine Resistance and Designing Novel Antimalarials." In Biophysical and Computational Tools in Drug Discovery. Springer International Publishing, 2021. http://dx.doi.org/10.1007/7355_2021_131.

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Conference papers on the topic "PHARMACOPHORE MODELING"

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Djokovic, Nemanja, Ana Postolovic, and Katarina Nikolic. "MOLECULAR MODELING OF 5‐[(AMIDOBENZYL)OXY]‐ NICOTINAMIDES AS SIRTUIN 2 INHIBITORS USING ALIGNMENT- (IN)DEPENDENT 3D-QSAR ANALYSIS AND MOLECULAR DOCKING." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.410dj.

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The group of 5‐[(amidobenzyl)oxy]‐nicotinamides represents promising group of sirtuin 2 (SIRT2) inhibitors. Despite structural similarity, representatives of this group of inhibitors displayed versatile mechanisms of inhibition which hamper rational drug design. The aim of this research was to form a 3D-QSAR (3D-Quantitative Structure-Activity Relationship) model, define the pharmacophore of this subgroup of SIRT2 inhibitors, define the mode of protein-ligand interactions and design new compounds with improved predicted activity and pharmacokinetics. For the 3D-QSAR study, data set was generat
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Shih, Kuei-Chung, Chun-Yuan Lin, Jiayi Zhou, Shih-Han Huang, and Chuan-Yi Tang. "Develop integration modeling approach for discovery neuraminidase inhibitors in silico based on pharmacophore and CoMSIA models." In 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2010. http://dx.doi.org/10.1109/bibmw.2010.5703855.

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Huo, Xiaoqian, Ludi Jiang, Xi Chen, Yusu He, Yongqiang Yang, and Yanling Zhang. "A combination of pharmacophore modeling, molecular docking and virtual screening for NPC1L1 receptor inhibitors from Chinese herbs." In 2014 8th International Conference on Systems Biology (ISB). IEEE, 2014. http://dx.doi.org/10.1109/isb.2014.6990429.

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Johari, Surabhi, Panchamita Basumatary, Kanwar Narain, Pratap Parida, and N. C. Barua. "Ligand-Based Pharmacophore Modeling, Virtual Screening and Molecular Docking Studies for Discovery of Novel Inhibitors against Staphylococcal Infections." In 2013 International Conference on Machine Intelligence and Research Advancement (ICMIRA). IEEE, 2013. http://dx.doi.org/10.1109/icmira.2013.131.

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Lengers, Isabelle, Fabian Herrmann, Samer Haidar, and Joachim Jose. "Human Hyal‑1 – from in silico Pharmacophore Modeling to in vitro Inhibitor Screening." In 3rd International Electronic Conference on Medicinal Chemistry. MDPI, 2017. http://dx.doi.org/10.3390/ecmc-3-04708.

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Cvijetić, Ilija, Miljan Bigović, Petar Ristivojević, Maja Vitorović-Todorović, Mire Zloh, and Dušanka Milojković-Opsenica. "THERMODYNAMICS OF THE ANTIOXIDANT ACTIVITY OF HUMULONES AND OTHER ANTIOXIDANTS FROM BEER – A MOLECULAR MODELING APPROACH." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.408c.

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Recent experimental study identified eight potent antioxidants in German beers, including isoxanthohumol, (R)- and (S)-adhumulone, cis– and trans-iso-adhumulone, cis– and trans-iso- n-humulone, and desdimetyhyl-octahydro-iso-cohumulone. To provide insights into the structural basis of their radical scavenging activity, we calculated the thermodynamic feasibility of two common antioxidant mechanisms, hydrogen atom transfer (HAT) and single electron transfer followed by proton transfer (SET-PT), using the density functional theory (DFT) with B3LYP/6-311g++(2d,2p) method in the gas phase and impl
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