Academic literature on the topic '3D-QSAR model'

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Journal articles on the topic "3D-QSAR model"

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Terzioglu, Nalan, and Hans-Dieter Höltje. "Receptor-Based 3D QSAR Analysis of Serotonin 5-HT1D Receptor Agonists." Collection of Czechoslovak Chemical Communications 70, no. 9 (2005): 1482–92. http://dx.doi.org/10.1135/cccc20051482.

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A three-dimensional quantitative structure-activity relationship study (3D QSAR) has been successfully applied to explain the binding affinities for the serotonin 5-HT1D receptor of a triptan series. The paper describes the development of a receptor-based 3D QSAR model of some known agonists and recently developed triptans on the 5-HT1D serotonergic receptor, showing a significant correlation between predicted and experimentally measured binding affinity (pIC50). The pIC50 values of these agonists are in the range from 5.40 to 9.50. The ligand alignment obtained from dynamic simulations was ta
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Zhao, Manman, Lin Wang, Linfeng Zheng, et al. "2D-QSAR and 3D-QSAR Analyses for EGFR Inhibitors." BioMed Research International 2017 (2017): 1–11. http://dx.doi.org/10.1155/2017/4649191.

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Epidermal growth factor receptor (EGFR) is an important target for cancer therapy. In this study, EGFR inhibitors were investigated to build a two-dimensional quantitative structure-activity relationship (2D-QSAR) model and a three-dimensional quantitative structure-activity relationship (3D-QSAR) model. In the 2D-QSAR model, the support vector machine (SVM) classifier combined with the feature selection method was applied to predict whether a compound was an EGFR inhibitor. As a result, the prediction accuracy of the 2D-QSAR model was 98.99% by using tenfold cross-validation test and 97.67% b
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Jagdale, Deepali M., and Ramaa C. S. "QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP ANALYSIS OF NOVEL PYRAZOLINE DERIVATIVES USING K NEAREST NEIGHBOUR MOLECULAR FIELD ANALYSIS METHOD." International Journal of Pharmacy and Pharmaceutical Sciences 9, no. 12 (2017): 87. http://dx.doi.org/10.22159/ijpps.2017v9i12.19401.

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Objective: Malonyl CoA decarboxylase (MCD) enzyme plays important role in fatty acid and glucose oxidation. Inhibition of MCD might turn to a novel approach to treat ischemia. The main objective of this research article was to develop a novel pharmacophore for enhanced activity.Methods: Three-dimensional quantitative structure-activity relationships (3D-QSAR) was performed for pyrazoline derivatives as MCD inhibitors using VLife MDS 4.6 software. The QSAR model was developed using the stepwise 3D-QSAR kNN-MFA method.Results: The statistical results generated from kNN-MFA method indicated the s
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Asgaonkar, K. D., S. M. Patil, T. S. Chitre, S. D. Wani, and M. T. Singh. "QSAR tool for optimization of nitrobenzamide pharmacophore for antitubercular activity." Bulletin of the Karaganda University. "Chemistry" series 105, no. 1 (2022): 60–68. http://dx.doi.org/10.31489/2022ch1/60-68.

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Tuberculosis (TB) is a leading cause of death worldwide from a single infectious agent, Mycobacterium tuberculosis (MTB), especially due to the development of resistant strains and its co-infections in HIV. Quantitative-structure activity relationship (QSAR) studies aid rapid drug discovery. In this work, 2D and 3D QSAR studies were carried out on a series of nitrobenzamide derivatives to design newer analogues for antitubercular activity. 2D QSAR was performed using MLR on a data set showing antitubercular activity. The 3D-QSAR studies were performed by kNN–MFA using simulated annealing varia
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Mishra, Puja, Sumit Nandi, Ankit Chatterjee, et al. "Development of 2D and 3D QSAR models of pyrazole derivatives as acetylcholine esterase inhibitors." Journal of the Serbian Chemical Society, no. 00 (2024): 39. http://dx.doi.org/10.2298/jsc230221039m.

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The drugs that are most useful in all stages of Alzheimer?s disease (AD) are acetylcholinesterase (AChE) inhibitors. The objectives of this work are to generate various QSAR models and to select robust predictive models from corresponding models. Studies were then focused on finding a range of pyrazole-like AChE inhibitors by 2D and 3D QSAR analysis. Genetic algorithm-based multiple linear regression (GA-MLR) provided the statistically robust 2D-QSAR model that depicted the significance of molecular volume and number of multiple bonds along with the presence/absence of specific atom-centred fr
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B.V.S, Suneel Kumar, Jagarlapudi A. R. P. Sarma, and Lakshmi Narasu. "3D-QSAR studies on Pyrido[2,3-d]pyrimidine Derivatives as Fibroblast Growth Factor Receptor 1 Inhibitors: Application of Molecular Field Analysis (MFA)." International Journal of Drug Design and Discovery 2, no. 4 (2024): 619–32. https://doi.org/10.37285/ijddd.2.4.2.

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Three-dimensional quantitative structure–activity relationship (3D-QSAR) models were developed for 77 pyrido[2,3-d]pyrimidines derivatives, inhibiting fibroblast growth factor receptor 1 (FGFR1). The QSAR model was developed using 56 compounds and its predictive ability was assessed using a test set of 21 compounds. The predictive 3D-QSAR models have conventional r2 values of 0.920 for MFA and the cross-validated coefficient r2cv values of 0.884 for MFA. The results of 3D-QSAR methodologies provide a powerful tool directed to the design of potent and selective pyrido[2,3-d]pyrimidines inhibito
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Ren, Ji-Xia, Rui-Tao Zhang, and Hui Zhang. "Identifying Novel ATX Inhibitors via Combinatory Virtual Screening Using Crystallography-Derived Pharmacophore Modelling, Docking Study, and QSAR Analysis." Molecules 25, no. 5 (2020): 1107. http://dx.doi.org/10.3390/molecules25051107.

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Autotaxin (ATX) is considered as an interesting drug target for the therapy of several diseases. The goal of the research was to detect new ATX inhibitors which have novel scaffolds by using virtual screening. First, based on two diverse receptor-ligand complexes, 14 pharmacophore models were developed, and the 14 models were verified through a big test database. Those pharmacophore models were utilized to accomplish virtual screening. Next, for the purpose of predicting the probable binding poses of compounds and then carrying out further virtual screening, docking-based virtual screening was
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Chhajed, Priyanka N., and Ravindra B. Patil. "Exploring 3D QSAR Study of Pyridone-Pyrimidone Derivatives as Glucokinase Activators in Treatment of Diabetes Mellitus by using CoMFA Method." Asian Journal of Organic & Medicinal Chemistry 7, no. 1 (2022): 42–54. http://dx.doi.org/10.14233/ajomc.2022.ajomc-p360.

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In this work, we have performed 3D QSAR study of reported pyridone-pyrimidone derivatives. CoMFA was applied to generate 3D QSAR models. Total eight QSAR models were generated. Model 2 was close to standard set criteria. Effect of steric and electrostatic substituents on biological activity was observed on contour maps. This study will be helpful for future researchers in designing new pyridinepyrimidone derivatives.
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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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Zhang, Jiaming, Qinqin Liu, Haoxia Zhao, Guiyu Li, Yunpeng Yi, and Ruofeng Shang. "Design and Synthesis of Pleuromutilin Derivatives as Antibacterial Agents Using Quantitative Structure–Activity Relationship Model." International Journal of Molecular Sciences 25, no. 4 (2024): 2256. http://dx.doi.org/10.3390/ijms25042256.

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The quantitative structure–activity relationship (QSAR) is one of the most popular methods for the virtual screening of new drug leads and optimization. Herein, we collected a dataset of 955 MIC values of pleuromutilin derivatives to construct a 2D-QSAR model with an accuracy of 80% and a 3D-QSAR model with a non-cross-validated correlation coefficient (r2) of 0.9836 and a cross-validated correlation coefficient (q2) of 0.7986. Based on the obtained QSAR models, we designed and synthesized pleuromutilin compounds 1 and 2 with thiol-functionalized side chains. Compound 1 displayed the highest a
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Dissertations / Theses on the topic "3D-QSAR model"

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Sköld, Christian. "Computational Modeling of the AT2 Receptor and AT2 Receptor Ligands : Investigating Ligand Binding, Structure–Activity Relationships, and Receptor-Bound Models." Doctoral thesis, Uppsala University, Organic Pharmaceutical Chemistry, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7823.

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<p>Rational conversion of biologically active peptides to nonpeptide compounds with retained activity is an appealing approach in drug development. One important objective of the work presented in this thesis was to use computational modeling to aid in such a conversion of the peptide angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). An equally important objective was to gain an understanding of the requirements for ligand binding to the Ang II receptors, with a focus on interactions with the AT<sub>2</sub> receptor.</p><p>The bioactive conformation of a peptide can provide important g
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Sköld, Christian. "Computational Modeling of the AT2 Receptor and AT2 Receptor Ligands : Investigating Ligand Binding, Structure–Activity Relationships, and Receptor-Bound Models." Doctoral thesis, Uppsala universitet, Avdelningen för organisk farmaceutisk kemi, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7823.

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Rational conversion of biologically active peptides to nonpeptide compounds with retained activity is an appealing approach in drug development. One important objective of the work presented in this thesis was to use computational modeling to aid in such a conversion of the peptide angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). An equally important objective was to gain an understanding of the requirements for ligand binding to the Ang II receptors, with a focus on interactions with the AT2 receptor. The bioactive conformation of a peptide can provide important guidance in peptidomi
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Alwassil, Osama I. "Elaboration and Design of α7 nAChR Negative Allosteric Modulators". VCU Scholars Compass, 2015. http://scholarscompass.vcu.edu/etd/3902.

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α7 Neuronal nicotinic acetylcholine receptors are one of two major classes of receptors responsible for cholinergic neurotransmission in the central nervous system. The existence of α7 neuronal nAChRs in different regions of the nervous system suggests their involvement in certain essential physiological functions as well as in disorders such as Alzheimer’s disease (AD), drug dependence, and depression. This project was aimed toward the discovery and development of small–molecule arylguanidines that modulate α7 nAChR function with improved subtype-selectivity through an allosteric approach. Id
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Peterson, Shane. "Improved CoMFA Modeling by Optimization of Settings : Toward the Design of Inhibitors of the HCV NS3 Protease." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8140.

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Pedreros, Riquelme América Beatriz. "Diseño racional de antibacterianos de núcleo 8-aril- mercapto-pirimidoisoquinolinquinonas basado en las herramientas de química medicinal de gráfica de craig y modelo 3D-QSAR/COMFA." Tesis, Universidad de Chile, 2017. http://repositorio.uchile.cl/handle/2250/144766.

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Memoria para optar al título de Químico Farmacéutico<br>A lo largo del tiempo, los antibacterianos han sido ampliamente utilizados en el tratamiento y control de enfermedades infecciosas. Actualmente la lucha contra varias enfermedades de origen bacteriano se ha vuelto un problema de salud a nivel mundial, debido a la resistencia bacteriana. Sumado a lo anterior, la tendiente disminución en investigación y desarrollo de nuevos antibacterianos nos insta a destinar los esfuerzos en investigar nuevos compuestos activos, idealmente, frente a bacterias multirresistentes, con una estructura química
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AbdulHameed, Mohamed Diwan Mohideen. "COMPUTATIONAL DESIGN OF 3-PHOSPHOINOSITIDE DEPENDENT KINASE-1 INHIBITORS AS POTENTIAL ANTI-CANCER AGENTS." UKnowledge, 2009. http://uknowledge.uky.edu/gradschool_diss/757.

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Computational drug design methods have great potential in drug discovery particularly in lead identification and lead optimization. 3-Phosphoinositide dependent kinase-1 (PDK1) is a protein kinase and a well validated anti-cancer target. Inhibitors of PDK1 have the potential to be developed as anti-cancer drugs. In this work, we have applied various novel computational drug design strategies to design and identify new PDK1 inhibitors with potential anti-cancer activity. We have pursued novel structure-based drug design strategies and identified a new binding mode for celecoxib and its derivati
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Schaal, Wesley. "Computational Studies of HIV-1 Protease Inhibitors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2002. http://publications.uu.se/theses/91-554-5213-2/.

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Chen, Kuan-Ju, and 陳冠如. "Applying 3D-QSAR technique to construct the pharmacophore model of farnesyltransferase inhibitors." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/52165476443295609708.

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碩士<br>國立清華大學<br>分子醫學研究所<br>96<br>Abstract A set of 68 imidazole and cyanophenyl containing farnesyltransferase (FTase) inhibitors were subjected to three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using the comparative molecular field analysis (CoMFA) , comparative molecular similarity indices analysis (CoMSIA), and a pharmacophore building method, the Catalyst program. The structures of these inhibitors were generated theoretically, and the conformations used in the 3D-QSAR studies were defined by docking them into the known structure of FTase binding pocket th
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Book chapters on the topic "3D-QSAR model"

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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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Ramalakshmi, N., S. Arunkumar, and Sakthivel Balasubramaniyan. "QSAR and Lead Optimization." In Advances in Medical Technologies and Clinical Practice. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7326-5.ch004.

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There are many diseases for which suitable drugs have not been identified. As the population increases and the environment gets polluted, new infections are reported. Random screening of synthesized compounds for biological activity is time consuming. QSAR has a prominent role in drug design and optimization. It is derived from the correlation between the physicochemical properties and biological activity. QSAR equations are generated using statistical methods like regression analysis and genetic function approximation. Both 2D parameters and 3D parameters are involved in generating the equati
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Mariappan, Gurusamy, and Anju Kumari. "Virtual Screening and Its Applications in Drug Discovery Process." In Advances in Medical Technologies and Clinical Practice. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7326-5.ch005.

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Virtual screening plays an important role in the modern drug discovery process. The pharma companies invest huge amounts of money and time in drug discovery and screening. However, at the final stage of clinical trials, several molecules fail, which results in a large financial loss. To overcome this, a virtual screening tool was developed with super predictive power. The virtual screening tool is not only restricted tool small molecules but also to macromolecules such as protein, enzyme, receptors, etc. This gives an insight into structure-based and Ligand-based drug design. VS gives reliable
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"Similarity-Based 3D-QSAR Models." In Three Dimensional QSAR. CRC Press, 2010. http://dx.doi.org/10.1201/b10419-11.

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de Souza, Anacleto S., Leonardo G. Ferreira, and Adriano D. Andricopulo. "2D and 3D QSAR Studies on a Series of Antichagasic Fenarimol Derivatives." In Pharmaceutical Sciences. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-1762-7.ch037.

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Chagas disease is one of the most important neglected tropical diseases. Endemic in Latin America, the disease is a global public health problem, affecting several countries in North America, Europe, Asia and Oceania. The disease affects around 8-10 million people worldwide and the limited treatments available present low efficacy and severe side effects, highlighting the urgent need for new therapeutic options. In this work, the authors developed QSAR models for a series of fenarimol derivatives exhibiting anti-T. cruzi activity. The models were constructed using the Hologram QSAR (HQSAR), Co
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Du, Meijin, Wenwen Gu, Xixi Li, Fuqiang Fan, and Yu Li. "Modification of Hexachlorobenzene to Molecules with Lower Long-Range Transport Potentials Using 3D-QSAR Models with a Full Factor Experimental Design." In Advances in Marine Biology. Elsevier, 2018. http://dx.doi.org/10.1016/bs.amb.2018.09.004.

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Conference papers on the topic "3D-QSAR model"

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Ragno, Rino, and Alessio Ragno. "db.3d-qsar.com. The first 3D QSAR models database." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.051r.

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Field-Based Three-Dimensiona Quantitative Strucutere-Activity Relationships (FB 3D QSAR) comprise computational approaches used in drug design and molecular modeling to analyze the relationship between the three-dimensional structure of a list of molecules (described by molecular interaction fields) and their associated biological activities (BAs). It aims to understand how different structural features of the molecules contribute to enhancing or lowering the biological potency. The process of FB 3D QSAR involves several steps. First, a dataset of structurally diverse molecules with known BAs
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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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Levovnik, Bojan D., Aleksa P. Alargić, Miloš M. Svirčev, and Goran I. Benedeković. "Building a 3D QSAR model with isopropylidene analogs of cytotoxic styryl-lactones." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.559l.

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Styryl-lactones are a class of natural products and related analogs that exhibit diverse biological activities, including anticancer, anti-inflammatory, and antimicrobial properties. Since these compounds are routinely obtained in our laboratory from their O-isopropylidene precursors, we envisioned the project to examine and compare their respective structures and in-vitro activities. This paper presents a basic 3D-QSAR steric model built on a small set of 11 selected O-isopropylidene and styryl-lactone (particularly [3.3.0]furofuranone) ligands and their in vitro activities against an MCF-7 c
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Boboriko, Natalia, He Liying, and Yaraslau Dzichenka. "THE EXPLORATION OF CYP17A1 LIGAND SPACE BY THE QSAR MODEL." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.439b.

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Cytochrome P450 17A1 (CYP17A1) is a critically important enzyme in humans that catalyzes the formation of all endogenous androgens. This enzyme is often considered a molecular target for the development of novel high efficient drugs against prostate cancer. In the present work, the random forest algorithm was used to conduct a QSAR study on 370 CYP17A1 ligands with different structures that were collected from the literature and databases, and a QSAR model was created based on the five important descriptors screened out – 2D adjacency and distance matrix descriptors, 2D atom counts and bond co
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Beljkas, Milan, Jelena Rebić, Milica Radan, Teodora Đikić, Slavica Oljačić, and Katarina Nikolic. "3D-Quantitative Structure-Activity Relationship and design of novel Rho-associated protein kinases-1 (ROCK1) inhibitors." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.584b.

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Rho-associated coiled-coil kinases (ROCKs) are involved in essential cellular functions such as adhesion, contraction, motility, proliferation, and cell survival/apoptosis. Four ROCK inhibitors have already been approved by the FDA and are used to treat glaucoma (ripasudil and netarsudil), cerebral vasospasm (fasudil), and graft-versus-host disease (belumosudil). Recent studies have focused on exploring the role of ROCK kinase inhibitors in cancer treatment and the development of new ROCK inhibitors. The main objective of this study was to identify critical structural features relevant to the
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