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Journal articles on the topic 'AutoDock Tools'

Author: Grafiati

Published: 2 June 2025

Last updated: 19 July 2025

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1

Sarthak, Pal1 Meenu Chaudhary*2 Kanishak Kala3. "Autodock & Autodock Vina: Development, Capabilities, & Applications in Molecular Docking." International Journal of Pharmaceutical Sciences 3, no. 5 (2025): 3005–19. https://doi.org/10.5281/zenodo.15458275.

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AutoDock and AutoDock Vina are popular molecular docking technologies that are essential to structure-based drug discovery because they can predict ligand-receptor interactions. Their theoretical underpinnings, methods of application, and comparative effectiveness across several biological targets are assessed in this study. Vina's multicore support and empirical scoring are compared to AutoDock4's semi-empirical scoring function and flexible docking strategy. Furthermore, the impact of developments like AutoGridFR and GPU-accelerated versions on computational efficiency is examined. The benef

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2

Flores, Doménica, and Carola Jerves. "Computational Comparison of the Binding Affinity of Selective and Nonselective NSAIDs to COX-2 Using Molecular Docking." Bionatura Journal 2, no. 2 (2025): 1–14. https://doi.org/10.70099/bj/2025.02.02.3.

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Cyclooxygenase-2 (COX-2) plays a key role in inflammation, making it a prime target for nonsteroidal anti-inflammatory drugs (NSAIDs). This study uses molecular docking to compare the binding affinities of four nonselective NSAIDs (aspirin, ibuprofen, diclofenac, naproxen) and three selective COX-2 inhibitors (celecoxib, rofecoxib, etoricoxib) to COX-2. Simulations with AutoDock4 and AutoDock Vina revealed distinct differences in binding profiles and selectivity. Selective COX-2 inhibitors exhibited stronger binding affinities, with etoricoxib achieving -11.22 kcal/mol (AutoDock4), driven by k

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Tang, Shidi, Ruiqi Chen, Mengru Lin, et al. "Accelerating AutoDock Vina with GPUs." Molecules 27, no. 9 (2022): 3041. http://dx.doi.org/10.3390/molecules27093041.

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AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best docking power among all the docking tools. Modern drug discovery is facing a common scenario of large virtual screening of drug hits from huge compound databases. Due to the seriality characteristic of the AutoDock Vina algorithm, there is no successful report on its parallel acceleration with GPUs. Current acceleration of AutoDock Vina typically relies on the stack of computing power as well as the allocation of resourc

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Zhang, Yuqi, Stefano Forli, Anna Omelchenko, and Michel F. Sanner. "AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools." Journal of Computational Chemistry 40, no. 32 (2019): 2882–86. http://dx.doi.org/10.1002/jcc.26054.

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Lestari, Ayu Rahmania, Irmanida Batubara, Setyanto Tri Wahyudi, and Auliya Ilmiawati. "Phenolic Compound in Garlic (Allium sativum) and Black Garlic Potency as Antigout Using Molecular Docking Approach." Jurnal Kimia Sains dan Aplikasi 25, no. 7 (2022): 253–63. http://dx.doi.org/10.14710/jksa.25.7.253-263.

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Phenolics, including flavonoids, are bioactive components in garlic in relatively abundant amounts and are present 2–4 times more in black garlic. Both of these compounds are reported to have biological activity, with one of them acting as an antioxidant. However, its ability as an antigout is still not widely reported. Xanthine oxidase, adenine deaminase, guanine deaminase, purine nucleoside phosphorylase, and 5-Nucleotidase II are involved during the production of uric acid and causes gout. This study predicted the potential of the phenolic and flavonoid compounds in garlic and black garlic

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Nawaz, Dil, TARIQ PERVEZ, and Muhammad Aqib Shabbir. "COMPARATIVE EVALUATION OF PROTEIN AND LIGAND-BASED DOCKING PROTOCOLS THROUGH PROTEIN PHOSPHATASE SLINGSHOT HOMOLOG 2 COMPLEX." Pakistan Postgraduate Medical Journal 34, no. 03 (2023): 139–44. http://dx.doi.org/10.51642/ppmj.v34i03.557.

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A molecular docking study is used to investigate the interactions between the two molecules. These interactions may be covalent, hydrogen, or Van der Waals forces. Various web-based and stand-alone tools have been discovered for molecular docking analysis. In this study, we performed a comparison between web-based and stand-alone docking tools to evaluate the accuracy. Five web-based tools i) Dockthor, ii) Patchdock, iii) RPBA Web, iv) Swissdock, v) Patinum and two stand-alone tools1) Autodock Vina & 2) Hex were selected for the evaluation of the tool`s accuracy in term of best conformatio

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Ayubbi, Muhammad Reza Pahlevy Al, Rika Melati, and Umul Karimah. "PENAMBATAN MOLEKUL SIANIDIN Ipomoea batatas L. SEBAGAI INHIBITOR HUMAN EPIDERMAL RECEPTOR 2 (HER-2) PADA KANKER PAYUDARA." Journal of Sustainable Transformation 1, no. 2 (2023): 60–67. http://dx.doi.org/10.59310/jst.v1i2.14.

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HER-2 (Human Epidermal Receptor 2) is a receptor on the cell surface that affects cell proliferation, this receptor support controls healthy cell growth,divide and repair cells when they are damaged. When HER-2 had overexpressed will not controlled cancer cell division. Overexpressed HER-2 could inhibited with cyanidine compound flavonoid derivatives from Ipomoea batatas L. (purple sweet potato). This study aim to measured potential of Ipomoea batatas L. cyanidin compounds in inhibited overexpressed HER-2 using computational chemistry methods specifically is molecular docking. Stages of molecu

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Namitha, K. N., and Velmurugan V. "Review of bioinformatic tools used in Computer Aided Drug Design (CADD)." World Journal of Advanced Research and Reviews 14, no. 2 (2022): 453–65. https://doi.org/10.5281/zenodo.7298898.

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Drug discovery is а time consuming рrосess of finding out a new drug molecule. The process takes many years to complete and needs human resource. These is difficulties have been overcome by introducing computer programmes in drug discovery (CADD) which includes target identification, hit identification, and molecular modification of а lead compound to optimize desired effects and minimize side effects, based on the knowledge of their biological targets. Molecular modelling is the process of designing a molecule with a computer-based collection of programmes (in-silico design) for deriving, rep

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Kenneth Obiakor, Onyeka Chinwuba Obidiegwu, Keziah Uchechi Ajah, Christian Chidebe, Ajuzie Henry Ogechi, and Ikemefuna Chijioke Uzochukwu. "Discovery of antiadhesins of Helicobacter pylori from existing drugs and medicines for malaria ventures pathogen box compounds." GSC Biological and Pharmaceutical Sciences 20, no. 3 (2022): 198–212. http://dx.doi.org/10.30574/gscbps.2022.20.3.0356.

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Background: Helicobacter pylori infection is a worldwide problem with more than half of the world's population in both developed and developing countries are infected with this organism. The best-characterized H. pylori adhesins, Blood group antigen binding Adhesin (BabA) and Sialic acid binding Adhesin (SabA) are virulent factors which facilitate adhesion of the bacteria to the host cells. Methods: We determined the binding affinities of selected existing drugs and medicines for malaria venture pathogen box compounds to H. pylori adhesin receptors by molecular docking simulations. The 3D crys

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Arakelian, Arina G., Gennady N. Chuev, and Timur V. Mamedov. "Molecular Docking of Endolysins for Studying Peptidoglycan Binding Mechanism." Molecules 29, no. 22 (2024): 5386. http://dx.doi.org/10.3390/molecules29225386.

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Endolysins of bacteriophages, which degrade the bacterial cell wall peptidoglycan, are applicable in many industries to deal with biofilms and bacterial infections. While multi-domain endolysins have both enzymatically active and cell wall-binding domains, single-domain endolysins consist only of an enzymatically active domain, and their mechanism of peptidoglycan binding remains unexplored, for this is a challenging task experimentally. This research aimed to explore the binding mechanism of endolysins using computational approaches, namely molecular docking and bioinformatical tools, and ana

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Saputra, Ziyan, Ai Susanti, Devona Ozora Toelle, et al. "PERBANDINGAN EFEKTIVITAS PARASETAMOL, FENASETIN, DAN ASETANILIDA SEBAGAI ANALGESIK DAN ANTI-INFLAMASI MENGGUNAKAN METODE MOLECULAR DOCKING." Dalton : Jurnal Pendidikan Kimia dan Ilmu Kimia 6, no. 1 (2023): 74. http://dx.doi.org/10.31602/dl.v6i1.9958.

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Abstrak.Parasetamol, fenasetin, dan asetanilida merupakan tiga senyawa yang sering digunakan sebagai analgesik dan anti-inflamasi. Perbandingan efektivitas ketiga senyawa tersebut dapat dipelajari menggunakan metode molecular docking. Reseptor diperoleh dari dari RCsB dengan PDB ID:COX6 kemudian disiapkan pada software AutoDock-Tools 1.5.6. Sedangkan ligan yang digunakan adalah parasetamol, fenasetin, dan asetanilida di unduh struktur 2D dalam format .pdbqt dari PubChem. Simulasi docking dilakukan melalui AutoDock Vina 1.1.2 yang tertanam di AutoDockTools 1.5.6. Hasil docking divisualisasikan

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12

Butt, Sania Safdar, Yasmin Badshah, Maria Shabbir, and Mehak Rafiq. "Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians." JMIR Bioinformatics and Biotechnology 1, no. 1 (2020): e14232. http://dx.doi.org/10.2196/14232.

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In the field of drug discovery, many methods of molecular modeling have been employed to study complex biological and chemical systems. Experimental strategies are integrated with computational approaches for the identification, characterization, and development of novel drugs and compounds. In modern drug designing, molecular docking is an approach that explores the confirmation of a ligand within the binding site of a macromolecule. To date, many software and tools for docking have been employed. AutoDock Vina (in UCSF [University of California, San Francisco] Chimera) is one of the computat

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Macari, Gabriele, Daniele Toti, Andrea Pasquadibisceglie, and Fabio Polticelli. "DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina." International Journal of Molecular Sciences 21, no. 24 (2020): 9548. http://dx.doi.org/10.3390/ijms21249548.

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Motivation: Bringing a new drug to the market is expensive and time-consuming. To cut the costs and time, computer-aided drug design (CADD) approaches have been increasingly included in the drug discovery pipeline. However, despite traditional docking tools show a good conformational space sampling ability, they are still unable to produce accurate binding affinity predictions. This work presents a novel scoring function for molecular docking seamlessly integrated into DockingApp, a user-friendly graphical interface for AutoDock Vina. The proposed function is based on a random forest model and

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Br Siagian, Dos D. L. E., Billy J. Kepel, Aaltje Manampiring, Widdhi Bodhi, Fatimawali Fatimawali, and Fona D. H. Budiarso. "Analisis Antioksidan Senyawa Bioaktif Ekstrak Lidah Buaya Secara Insilico." Jurnal e-Biomedik 10, no. 2 (2023): 129–35. http://dx.doi.org/10.35790/ebm.v10i2.46334.

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Abstract: Aloe vera (Aloe vera L.) is a functional plant that is often found and has a wide range of health advantages. Antioxidants are chemical molecules that inhibit free radicals in the body, which can cause disease by generating oxidation events that destroy cell structure and function. The goal of this research is to see how bioactive chemicals from the aloe vera plant (Aloe vera L.) interact with antioxidant activity. The molecular docking method is combined with insilico analysis in this study, which employs four key applications: autodock tools, autodock vina, biovia discovery studio,

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15

El Aissouq, Abdellah, Oussama Chedadi, Mohammed Bouachrine, and Abdelkrim Ouammou. "Identification of Novel SARS-CoV-2 Inhibitors: A Structure-Based Virtual Screening Approach." Journal of Chemistry 2021 (February 8, 2021): 1–7. http://dx.doi.org/10.1155/2021/1901484.

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The recent outbreak of the coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the last few months raised global health concern. Previous research described that remdesivir and ritonavir can be used as effective drugs against COVID-19. In this study, we applied the structure-based virtual screening (SBVS) on the high similar remdesivir- and ritonavir-approved drugs, selected from the DrugBank database as well as on a series of ritonavir derivatives, selected from the literature. The aim was to provide new potent SARS-CoV-2 main protease

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Pebrianti, Denayu, Juni Ekowati та Dhea Ananda Ainurrizma. "Molecular Docking Study of Ferulic Acid Analog Compounds as Lung Antifibrotic at TGF-β1 Receptors". Berkala Ilmiah Kimia Farmasi 10, № 1 (2023): 7–12. http://dx.doi.org/10.20473/bikfar.v10i1.45430.

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Pulmonary fibrosis is one of the conditions that occur in Post-COVID Syndrome patients. Development of specific treatment as an agent to treat pulmonary fibrosis is still ongoing. Ferulic acid is a compound that has a potential lung antifibrotic agent through inhibition of TGF-β1-mediated signaling. Molecular docking studies using the AutoDock Tools program version 1.5.7 were conducted on ferulic acid and its analogs to determine the activity of compounds as antifibrotic. Furthermore, the interaction of the compound with the receptor was visualized using the Discovery Studio 2021 program. The

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17

Kenneth, Obiakor, Chinwuba Obidiegwu Onyeka, Uchechi Ajah Keziah, Chidebe Christian, Henry Ogechi Ajuzie, and Chijioke Uzochukwu Ikemefuna. "Discovery of antiadhesins of Helicobacter pylori from existing drugs and medicines for malaria ventures pathogen box compounds." GSC Biological and Pharmaceutical Sciences 20, no. 3 (2022): 198–212. https://doi.org/10.5281/zenodo.7142478.

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<strong>Background</strong>: <em>Helicobacter pylori</em> infection is a worldwide problem with more than half of the world's population in both developed and developing countries are infected with this organism. The best-characterized <em>H. pylori</em> adhesins, Blood group antigen binding Adhesin (BabA) and Sialic acid binding Adhesin (SabA) are virulent factors which facilitate adhesion of the bacteria to the host cells. <strong>Methods</strong>: We determined the binding affinities of selected existing drugs and medicines for malaria venture pathogen box compounds

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18

Syahputra, H. D., M. Masfria, P. A. Z. Hasibuan, and I. Iksen. "IN SILICO DOCKING STUDIES OF PHYTOSTEROL COMPOUNDS SELECTED FROM Ficus religiosa AS POTENTIAL CHEMOPREVENTIVE AGENT." RASAYAN Journal of Chemistry 15, no. 02 (2022): 1080–84. http://dx.doi.org/10.31788/rjc.2022.1526801.

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Traditional medicine has employed Ficus reliosa (Moraceae) to treat a wide range of diseases such as central nervous system disorder, infectious disease, endocrine system, respiratory system, etc. This study aimed to evaluate phytosterol constituents that may serve as lead-drug such as 28-Isofucosterol, Stigmasterol, Sitosterol, and Campesterol towards their pharmacokinetic properties and chemopreventive activity to regulate nuclear receptor factor 2 (Nrf2) uptake bound by Kelch-like Activating Protein (Keap1). Structures were studied to evaluate their respective bioactivity using Milliprot fo

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Renadi, Sedin, Anindita Tri Kusuma Pratita, Richa Mardianingrum, and Ruswanto Ruswanto. "The Potency of Alkaloid Derivates as Anti-Breast Cancer Candidates: In Silico Study." Jurnal Kimia Valensi 9, no. 1 (2023): 89–108. http://dx.doi.org/10.15408/jkv.v9i1.31481.

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Breast cancer is the most frequent malignancy in women worldwide. One of the target receptors for the treatment of breast cancer are estrogen, progesterone, and HER2 receptors. An alternative treatment using natural ingredients has been developed, one of which is alkaloid compounds. This study aims to determine the activity of alkaloid compounds as anti-breast cancer agents through an in-silico method. Virtual screening (AutoDock Vina), molecular docking (AutoDock Tools), molecular dynamics (Desmond), scanning Lipinski's rule of five, as well as pharmacokinetic and toxicity parameters, were pe

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Wiratama, Minandre, and Cornelia Budimarwanti. "Synthesis and Molecular Docking Study of Dibenzal Monocarbonyl (Curcumin Analog) and Its Potential as Anti-Inflammatory." Jurnal Kimia Sains dan Aplikasi 28, no. 2 (2025): 68–72. https://doi.org/10.14710/jksa.28.2.68-72.

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Curcumin is a naturally occurring substance with a wide range of biological activity. One of the biological activities of curcumin is as an anti-inflammatory. The science of organic synthesis is able to produce substances that are analogous to those found in nature. The synthesis of organic compounds can also be used to change a compound by making it more bioactive. This research focused on synthesizing dibenzal monocarbonyl, a compound similar to curcumin, and examined its interaction with the active site of cyclooxygenase-2 (COX-2) through molecular docking simulations. Dibenzal monocarbonyl

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Saji, Christy, Rajeswary K. Balachandran, Aneeza M. Nizar, et al. "MOLECULAR DOCKING STUDIES WITH PHYTOCONSTITUENTS OF TINOSPORA SINENSIS TARGETING SARS-COV-2 PROTEIN USING AUTODOCK VINA." INDIAN DRUGS 62, no. 05 (2025): 22–27. https://doi.org/10.53879/id.62.06.15489.

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Drug discovery is time-consuming and resource-intensive, but computational approaches offer a more efficient alternative. The urgency for antiviral treatments became evident during the SARS-CoV-2 pandemic due to the virus’s rapid spread and mutations. This study utilizes computational drug design techniques to assess the antiviral potential of Tinospora sinensis constituents against the SARS-CoV-2 main protease (PDB ID: 6LU7). The target protein was prepared using AutoDock tools, and molecular docking was conducted with AutoDock Vina. Of 37 compounds, 5 exhibited a binding affinity below -7 kc

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Saini, Rita, Mayank Yadav, Ranjit Singh, and Mukesh Maithani. "Novel 1,2-Disubstituted Benzimidazole Derivatives: Synthesis and in silico Antibacterial Activity." Asian Journal of Chemistry 36, no. 11 (2024): 2615–21. http://dx.doi.org/10.14233/ajchem.2024.32592.

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A series of 14 novel 1,2-disubstituted benzimidazole derivatives was synthesized by reacting substituted benzimidazoles with ethyl succinyl chloride and characterized by spectroscopic techniques (FTIR, 1H NMR and Mass). The molecular docking analyses with AutoDock Tools-1.5.7 were used to examine the interactions between the compounds and the active site residues of Topoisomerase-II enzyme (PDB ID: 1JIJ). Amongst the 14 derivatives, 11 derivatives had shown greater binding affinity with the receptor in comparison with standard drug pefloxacin.

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Amelia, Marsha Anggita, Dini Kesuma, Aguslina Kirtishanti, I. Gede Ari Sumartha, and Maria Claudya. "Molecular Docking: Study of Chalcone Derivatives from Boesenbergia pandurata Targeting Estrogen Receptor Alpha (ER–a) for Breast Cancer." Jurnal Penelitian Pendidikan IPA 10, no. 11 (2024): 8376–86. https://doi.org/10.29303/jppipa.v10i11.8734.

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The increasing number of cancer patients and the challenge of multidrug resistance (MDR) demand more effective drugs, which can be developed by modifying compounds derived from natural resources, such as the flavonoid-rich temu kunci rhizome (Boesenbergia pandurata (Roxb.) Schlecht.). This study aims to predict the cytotoxicity and toxicity of 20 Pinostrobin derivatives and 19 Chalcone derivatives as potential anticancer candidates. Estrogen receptor alpha (ER-α), a validated cancer therapy target, was used for molecular docking in in silico tests using Molecular Graphics Laboratory (MGL) Tool

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Reynoso-García, María Fernanda, Dulce E. Nicolás-Álvarez, A. Yair Tenorio-Barajas, and Andrés Reyes-Chaparro. "Structural Bioinformatics Applied to Acetylcholinesterase Enzyme Inhibition." International Journal of Molecular Sciences 26, no. 8 (2025): 3781. https://doi.org/10.3390/ijms26083781.

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Acetylcholinesterase (AChE) is a critical enzyme involved in neurotransmission by hydrolyzing acetylcholine at the synaptic cleft, making it a key target for drug discovery, particularly in the treatment of neurodegenerative disorders such as Alzheimer’s disease. Computational approaches, particularly molecular docking and molecular dynamics (MD) simulations, have become indispensable tools for identifying and optimizing AChE inhibitors by predicting ligand-binding affinities, interaction mechanisms, and conformational dynamics. This review serves as a comprehensive guide for future research o

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Galal, Noha, Botros Y. Beshay, Omar Soliman, et al. "Evaluating the structure-based virtual screening performance of SARS-CoV-2 main protease: A benchmarking approach and a multistage screening example against the wild-type and Omicron variants." PLOS ONE 20, no. 2 (2025): e0318712. https://doi.org/10.1371/journal.pone.0318712.

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COVID-19 still poses a worldwide health threat due to continuous viral mutations and potential resistance to vaccination. SARS-CoV-2 viral multiplication hindrance by inhibiting the viral main protease (Mpro) deemed propitious. Structure-based virtual screening (SBVS) is a conventional strategy for discovering new inhibitors. Nonetheless, the SBVS efforts against Mpro variants needed to be benchmarked. Herein, in the first stage of the study, we evaluated four docking tools (FRED, PLANTS, AutoDock Vina and CDOCKER) via an in-depth benchmarking approach against SARS-CoV2 Mpro of both the wild t

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Zaelani, Bella Fatima Dora, Mega Safithri, and Dimas Andrianto. "Molecular Docking of Red Betel (Piper crocatum Ruiz & Pav) Bioactive Compounds as HMG-CoA Reductase Inhibitor." Jurnal Kimia Sains dan Aplikasi 24, no. 3 (2021): 101–7. http://dx.doi.org/10.14710/jksa.24.3.101-107.

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Cholesterol plaque buildup in artery walls occurs due to oxidation of Low-Density Lipoprotein (LDL) molecules by free radicals, which are a risk factor for coronary heart disease. Piper crocatum contains active compounds that can act as HMG-CoA reductase inhibitors, such as flavonoids, alkaloids, polyphenols, tannins, and essential oils. This study aimed to predict the potential of Piper crocatum extract and fraction compounds as HMG-CoA reductase inhibitors by investigating the ligand affinity to the HMG-CoA reductase enzyme. Ligand and receptor preparation was conducted using BIOVIA Discover

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Riza, Hafrizal, Andhi Fahrurroji, Arif Wicaksono, Ahmad Kharis Nugroho, and Sudibyo Martono. "DOCKING STUDY OF METHYL HESPERIDIN AS NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR." International Journal of Pharmacy and Pharmaceutical Sciences 10, no. 3 (2018): 85. http://dx.doi.org/10.22159/ijpps.2018v10i3.22724.

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Objective: This study aims to analyze the methyl hesperidin physicochemical properties related to solubility and permeability, and the affinity of methyl hesperidin against reverse transcriptase HIV-1 activity as a competitive substrate.Methods: This research was conducted using the computerized method, ChemOffice 15.0, to predict ligand physicochemical properties related to solubility and permeability, and Autodock Vina with Autodock Tools program to analyze ligand-receptor affinity.Results: The analysis result of physicochemical properties of hesperidin and methyl hesperidin is respectively

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I. Namirah, Fadilah, S. Dewi, F. V. I. de Lima, and N. S. Hardiany. "SENOLYTIC ACTIVITY EVALUATION OF CORIANDER (Coriandrum sativum L) PHYTOCONSTITUENTS: In-silico STUDY." RASAYAN Journal of Chemistry 15, no. 04 (2022): 2584–90. http://dx.doi.org/10.31788/rjc.2022.1547007.

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Coriander phytoconstituent has pro-apoptotic and anti-inflammatory activities. This study evaluated the activity of Coriander phytoconstituent against the Senescent Cell Anti-Apoptotic Pathways (SCAPs) network nodes that serve as targets for senolytic drugs. Docking simulations were performed using Autodock Vina PyRx (v0.8), Autodock Tools 1.5.6, and visualized by the Discovery Studio Visualizer. The anti-apoptotic protein (BCL-XL, BCL-2, BCLW, and survivin) interaction network was obtained from String db.org. The flavonoid compounds showed good binding energy than non-flavonoid compounds. In

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Harun, Sarahani, Nor Afiqah-Aleng, Fatin Izzati Abdul Hadi, Su Datt Lam, and Zeti-Azura Mohamed-Hussein. "Identification of Potential Genes Encoding Protein Transporters in Arabidopsis thaliana Glucosinolate (GSL) Metabolism." Life 12, no. 3 (2022): 326. http://dx.doi.org/10.3390/life12030326.

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Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana, the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and serves to protect high-value tissues such as reproductive tissues. This study aimed to identify potential GSL-transporter proteins (TPs) using a network-biology approach. The known A. thaliana GSL genes were retrieved from the literature and pathway databases and searched against several co-expression databases to generate a gene network consisting

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Kurniawan, Ilham, Laksmi Ambarsari, Popi Asri Kurniatin, and Setyanto Tri Wahyudi. "Novel Compounds Design of Acertannin, Hamamelitannin, and Petunidin-3-Glucoside Typical Compounds of African Leaves (Vernonia amygdalina Del) as Antibacterial Based on QSAR and Molecular Docking." Jurnal Jamu Indonesia 8, no. 2 (2024): 29–38. http://dx.doi.org/10.29244/jji.v8i2.326.

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Antibacterial secondary metabolites such as tannins and their derivatives are found in the Vernonia amygdalina Del. Antibiotic resistance can develop due to overuse, reducing the efficacy of drugs to prevent and treat infections. This research aims to use the Quantitative Structure-Activity Relationship (QSAR) and the semi-empirical method Austin Model 1 (AM1) to design a modified novel compound from African leaves that has improved antibacterial activity. This research includes a descriptor calculation of QSAR using AM1 MOE on typical compounds from African leaves, and calculation results are

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Zhang, Huyang, and Wenjuan Hou. "The Investigation of LPA Binding Sites on LPA 1 And LPA 4." Highlights in Science, Engineering and Technology 45 (April 18, 2023): 151–59. http://dx.doi.org/10.54097/hset.v45i.7337.

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Lysophosphatidic acid (LPA) is a class of biologically active lipid molecules with important biological functions. LPA can induce various cellular responses through six LPA receptors (LPA1-6) on cell membranes to achieve its biological functions. This study utilized computer simulation tools such as AutoDock Vina and RosettaFold to investigate the binding sites of LPA1 and LPA4 to LPA molecules. Based on these results, this study could provide new insights for the subsequent development of extracellular antagonists and agonists, and facilitate drug formation for the treatment of cancer invasio

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Anjum, Farah, Hamsa Jameel Banjer, Nahed Hawsawi, et al. "Exploring Natural Compounds Targeting the Bacterial SHV Protein to Combat Antibiotic Resistance: A Biocomputational Study." Advancements in Life Sciences 11, no. 4 (2024): 822. http://dx.doi.org/10.62940/als.v11i4.2919.

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Background: Antibiotic-resistant (AR) bacteria are rapidly spreading worldwide, posing a serious threat to antibiotic efficacy. Bacterial infections have emerged as a persistent threat following decades of antibiotic use. Sulfhydryl variable (SHV) is a well-known bacterial enzyme linked to AR. SHV has a high degree of genetic diversity, resulting in the existence of numerous distinct variants. Methods: The PyRx AutoDock VINA was used to conduct in-silico screening of a natural compound library to assess their interaction with the SHV-1 protein. SwissADME web tools were used to predict the phys

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Ullah, Hamid, Sadia Majid, Asma Abro та ін. "Synthesis and molecular docking analysis of MBH adducts' derived amides as potential β-lactamase inhibitors". Bioinformation 20, № 5 (2024): 449–59. http://dx.doi.org/10.6026/973206300200449.

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Humans suffer from various diseases that require more specific drugs to target them. Among the different potent agents, β-lactamases serve as good antibacterial agents; however, β-lactamases are resistant to such antibiotics. The present study was designed to prepare efficient β-lactamase inhibitor amides (12-15) from inexpensive, easily accessible, and bioactive precursors; Morita Baylis Hillman (MBH) adducts (5-8). The adducts (5-8) were primarily prepared by treating their respective aldehydes with the corresponding acrylate in the presence of an organic Lewis base at ambient temperature. T

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Kumari, Uma, Nehal Balhara, and Ojas Singh. "Computer Aided Drug Designing Approach for Prospective Human Metastatic Cancer." International Journal for Research in Applied Science and Engineering Technology 11, no. 7 (2023): 1874–79. http://dx.doi.org/10.22214/ijraset.2023.550014.

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Abstract: It is well known that finding new drugs is a difficult, expensive, time-consuming, and expensive project. According to a study, the typical time and cost for developing a new medicine through the conventional drug development pipeline is 12 years and 2.7 billion dollars. The pharmaceutical industry is grappling with the difficult and pressing challenge of how to find new drugs faster and at lower research costs.Insilico,The field of computer-aided drug discovery (CADD) has shown significant promise as an advanced technology for secure, cost-effective, and efficient drug design. In re

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Romadhan, Muhammad Despriansyah, Putri Mahirah Afladhanti, and Ni Made Dyah Gayatri. "Identifikasi Senyawa Aktif Pala (Myristica fragrans) sebagai Terapi Komplementer Antihipertensi melalui Penghambatan Reseptor ACE: Sebuah Studi Penambatan Molekuler." Jurnal Sains dan Kesehatan 5, no. 3 (2023): 339–49. http://dx.doi.org/10.25026/jsk.v5i3.1737.

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Hipertensi merupakan salah satu masalah kesehatan terbesar yang menjadi penyebab utama kematian di seluruh dunia. Angiotensin converting enzyme inhibitor (ACE-I) sebagai obat antihipertensi yang umum diketahui memiliki efek samping yang sering dikeluhkan. Penelitian ini bertujuan untuk mengidentifikasi senyawa potensial yang berasal dari pala (Myristica fragrans) sebagai antihipertensi dengan menggunakan studi penambatan molekular. Dua puluh tiga senyawa pala bersama dengan captopril digunakan dalam penelitian ini melalui pencarian literatur dan penyaringan daring. Senyawa dan obat pembanding

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Jagtap, Monali, Ghanshyam Girnar, and Vanshika Ahuja. "Computational Approaches to Molecular Docking and Protein Modeling in Drug Discovery." Journal of Drug Delivery and Therapeutics 15, no. 6 (2025): 278–87. https://doi.org/10.22270/jddt.v15i6.7212.

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Protein modeling and molecular docking are crucial computational methods in contemporary drug discovery. To identify potential therapeutic possibilities with high affinity and specificity, molecular docking predicts the ideal binding interactions between tiny molecules (ligands). The best binding interactions between target macromolecules, such proteins, and tiny molecules, or ligands, are predicted by molecular docking. When experimental structures are not accessible, protein modeling—including homology modeling and ab initio techniques—allows for the creation of three-dimensional protein str

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Emmanuel Chuks Oranu, IC Uzochukwu, Ebere Ifejirika Ezeonyi, et al. "Binding affinities and molecular dynamics simulations of selected approved drugs and Mucuna pruriens phytoconstituents with Escherichia coli Shiga toxin." GSC Biological and Pharmaceutical Sciences 30, no. 2 (2025): 029–35. https://doi.org/10.30574/gscbps.2025.30.2.0038.

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Shiga toxin (Stx)–producing Escherichia coli (STEC), also known as “verocytotoxin- producing E. coli” is a major food and waterborne pathogen of zoonotic origin. STEC infection is involved in several life-threatening disease conditions that includes diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome. We determined the binding affinities of selected approved drugs and Mucuna pruriens phytoconstituents to shiga toxin and ricin receptors (a toxin similar in structure to shiga toxin) by molecular docking simulations. The 3D crystal structures of Stx1, Stx2 and ricin receptor were obtaine

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Pham, Han Thi Ngoc, and Huong Thi Thu Phung. "Comparing the Performance of Molecular Docking Tools for HIV-1 Protease Inhibitors." Journal of Advanced Engineering and Computation 7, no. 2 (2023): 95. http://dx.doi.org/10.55579/jaec.202372.400.

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Human immunodeficiency virus (HIV) continues to pose a significant public health threat worldwide, disproportionately aﬀecting marginalized and vulnerable populations despite advancements in prevention and treatment. One promising approach in the development of antiretroviral therapies is the inhibition of HIV-1 protease, a key enzyme in the virus life cycle. To this end, we evaluated 23 known inhibitors of HIV-1 protease using three docking methods - Autodock 4.2 (AD4), AutoDockVina (Vina), and a modified Vina (mVina)- and found that all three methods produced reasonable binding affinities fo

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Quiroga, Diego. "Employing Molecular Docking Calculations for the Design of Alkyl (2-Alcoxy-2-Hydroxypropanoyl)-L-Tryptophanate Derivatives as Potential Inhibitors of 11β-Hydroxysteroid Dehydrogenase Type 1 (11β-HSD1)". Reactions 4, № 1 (2023): 108–16. http://dx.doi.org/10.3390/reactions4010006.

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In this paper, we presented the design by computational tools of novel alkyl (2-alcoxy-2-hydroxypropanoyl)-L-tryptophanate derivatives, which can be potential inhibitors of 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1). The molecular structure optimization of a group of 36 compounds was performed employing DFT-B3LYP calculations at the level 6-311G(d,p). Then, molecular docking calculations were performed using Autodock tools software, employing the Lamarckian genetic algorithm (LGA). Four parameters (binding, intermolecular and Van Der Waals hydrogen bonding desolvation energies, and HOM

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Ferdian, Pamungkas Rizki, Rizki Rabeca Elfirta, Azra Zahrah Nadhirah Ikhwani, et al. "Studi In Silico Senyawa Fenolik Madu sebagai Kandidat Inhibitor Mpro SARS-CoV-2." Media Penelitian dan Pengembangan Kesehatan 31, no. 3 (2021): 213–32. http://dx.doi.org/10.22435/mpk.v31i3.4920.

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SARS-CoV-2 has caused a global COVID-19 pandemic since late 2019 and the reported cases have not ended until now. One way to overcome the Covid-19 pandemic is to find the main viral protease inhibitor (Mpro) SARS-CoV-2 which is a key enzyme of virus replication. Honey is a bee-derived product that contains various phenolic compounds and has antiviral activity. This study aimed to find candidate Mpro SARS-CoV-2 inhibitors from honey phenolic compounds using molecular docking simulations in a directed manner. A total of 27 test ligands (from honey’s phenolic compounds), 4 comparison ligands (fro

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PHAM, Quan Minh, Thi Thuy Huong Le, Thi Hong Minh Pham, et al. "Molecular docking tutorial using AutoDock 4.2.6 on SARS-CoV-2 main protease for beginner." Vietnam Journal of Science and Technology 60, no. 6 (2022): 929–47. http://dx.doi.org/10.15625/2525-2518/16459.

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The worldwide pandemic caused by coronavirus SARS-CoV-2 (so called as COVID-19 disease) has affected 219 countries and territories, leading to numerous deaths and global financial crisis. The main protease (Mpro) of SARS-CoV-2 plays an important role in mediating the transcription and replication of virus, thus, one of the main therapeutic is to find compounds that are capable of inhibiting these enzymes as soon as possible. Nowadays, computer-aided drug design plays an important role in the field of drug discovery. In particular, molecular docking is one of the initial steps that effectively

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Alhassan, A. M., and I. Malami. "In Silico Screening of Sesquiterpene Lactones as Aldose Reductase Inhibitors." Nigerian Journal of Basic and Applied Sciences 28, no. 2 (2021): 64–69. http://dx.doi.org/10.4314/njbas.v28i2.8.

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Aldose reductase, a key enzyme of the polyol pathway catalyses NADPH-dependent reduction of glucose to sorbitol. Increased activity of this enzyme is considered a major factor contributing to the development of diabetic complications hence could be an important target in the treatment of these complications. In this work, a database of sesquiterpenes was prepared and screened for their drug-like properties based on the Lipinski’s rule of 5. The co-crystallised structure of aldose reductase was obtained from the Protein Databank and prepared for docking. In silico docking experiments was perfor

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Wiratama, Minandre, Stephanus Satria Wira Waskitha, Winarto Haryadi, and Tutik Dwi Wahyuningsih. "Synthesis, antimalarial activity assay and molecular docking study of N-substituted chloro-pyrazolines." Tropical Journal of Pharmaceutical Research 21, no. 6 (2022): 1255–61. http://dx.doi.org/10.4314/tjpr.v21i6.18.

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Purpose: To synthesize chloro-pyrazolines (A–D), determine their antimalarial activity against Plasmodium falciparum strain 3D7 in vitro, and understand the interaction between falcipain-2 active sites and synthesized compounds by molecular docking simulation.Methods: Chloro-pyrazolines (A–D) were synthesized via cyclo-condensation of 4-chloro chalcone derivatives using several types of hydrazines, i.e., formylhydrazine, benzoylhydrazine, phenylhydrazine and chlorophenylhydrazine. The compounds were analyzed and subjected to antimalarial assay against P. falciparum 3D7. Molecular docking was p

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Sengupta, Sounok, Ratul Bhowmik, Satarupa Acharjee, and Suchandra Sen. "http://www.biotech-asia.org/vol18no2/in-silico-modelling-of-1-3-3-substituted-phenyl-prop-2-enoyl-phenyl-thiourea-against-anti-inflammatory-drug-targets/." Biosciences Biotechnology Research Asia 18, no. 2 (2021): 413–21. http://dx.doi.org/10.13005/bbra/2928.

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The main objective of this present study was to analyze the anti-inflammatory activity of the compound 1- 3- [3-(substituted phenyl) prop-2-enoyl) phenyl thiourea against inflammation receptors Secretory Phospholipase A2 (sPLA2-X), Cyclooxygenase-2 (COX-2), Interleukin-1 Receptor-associated Kinase 4 (IRAK4), Tumor Necrosis Factor (TNF-alpha) and Inducible Nitric Oxide Synthase 4 using various in-silico techniques. The 3D structures of the receptors were retrieved from Protein Data Bank in PDB format. The ligand molecule was sketched in Chemdraw Ultra v 10.0. The proteins and the ligand molecul

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Li, Yang, Wei Zheng, Wuyun Qiqige, Shujuan Cao, Jishou Ruan, and Yanping Zhang. "A Novel Method for Drug Screen to Regulate G Protein-Coupled Receptors in the Metabolic Network of Alzheimer’s Disease." BioMed Research International 2018 (2018): 1–10. http://dx.doi.org/10.1155/2018/5486403.

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Alzheimer’s disease (AD) is a chronic and progressive neurodegenerative disorder and the pathogenesis of AD is poorly understood. G protein-coupled receptors (GPCRs) are involved in numerous key AD pathways and play a key role in the pathology of AD. To fully understand the pathogenesis of AD and design novel drug therapeutics, analyzing the connection between AD and GPCRs is of great importance. In this paper, we firstly build and analyze the AD-related pathway by consulting the KEGG pathway of AD and a mass of literature and collect 25 AD-related GPCRs for drug discovery. Then the ILbind and

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Hasan, Rahmawaty, and Rina Herowati. "Molecular Docking and Pharmacokinetic Studies of Moringa oleifera As Angiotensin-Converting Enzyme Inhibitors." JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA 11, no. 1 (2024): 80–88. http://dx.doi.org/10.20473/jfiki.v11i12024.80-88.

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Background: Hypertension in pregnancy is a vascular disorder that occurs before pregnancy or arises during pregnancy that there were 30% of cases of maternal death. Moringa oleifera's potential to lower blood pressure can be utilized as an alternative antihypertensive during pregnancy, minimizing the risk of preeclampsia. Objective: The purpose of this study was to determine the molecular target of Moringa oleifera is intended to optimize pharmacodynamic activity based on the interaction pattern of the compounds with the ACE inhibitor (PDB ID: 1O86). Methods: Molecular docking is carried out u

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I. Handayani, Supri, Rahmiati Rahmiati, Lisnawati Rahmadi, Rosmalena Rosmalena, and Vivitri D. Prasasty. "Molecular Docking and Drug-Likeness for the Identification of Inhibitory Action of Acetogenins from Annona muricata as Potential Anticancer against Hypoxia Inducible Factor 1 Alpha." Biomedical and Pharmacology Journal 11, no. 3 (2018): 1301–7. http://dx.doi.org/10.13005/bpj/1492.

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Hypoxia inducible factor 1 alpha (HIF-1α) regulates cell growth and differentiation which is implicated in human cancers. HIF-1α activates its cascade carcinogenesis mechanism in cancer cells. It is well-understood that signaling is initiated by HIF-1α receptor. Overexpression of HIF-1α is associated with several different human cancers, including breast cancer, lung cancer and colon cancer. Thus, HIF-1α becomes potential target of therapeutic approach in developing HIF-1α inhibitors. The aim of this research is to investigate potential inhibitors which are known as Acetogenins (AGEs) isolated

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Corbo, Tarik, Merima Miralem, Abdurahim Kalajdzic, and Naris Pojskic. "In silico prediction of the inhibitory effect of phytochemical components extracted from Knautia sarajevensis on the main protease of SARS-CoV-2 virus." Genetics & Applications 6, no. 2 (2022): 31–40. http://dx.doi.org/10.31383/ga.vol6iss2ga03.

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Essential role in replication and transcription of coronavirus makes the main protease of SARS-CoV-2 a great traget for drug design. The aim of this study was to predict structural interactions of compounds isolated from the Bosnian-Herzegovinian endemic plant Knautia sarajevensis (G. Beck) Szabó against the 3CLpro of SARS-CoV-2 virus. The three-dimensional crystal structure of SARS-CoV-2 main protease was retrieved from the RCSB Protein Data Bank and the three-dimensional structures of isolated compounds were obtained from the PubChem database. Active site was predicted using PrankWeb, while

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Hamzah, Haidar Ali, Junoretta Haviva Ernanto, Putri Mahirah Afladhanti, and Theodorus Theodorus. "POTENSI DAUN TEH HIJAU (Camellia sinensis) SEBAGAI INHIBITOR MAIN PROTEASE (Mpro) COVID-19: SEBUAH STUDI MOLECULAR DOCKING." Jurnal Ilmiah Ibnu Sina (JIIS): Ilmu Farmasi dan Kesehatan 7, no. 2 (2022): 212–22. http://dx.doi.org/10.36387/jiis.v7i2.789.

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Green tea is an herbal plant that has active compounds including anti-inflammatory, antioxidant, anti-allergic, and antiviral compounds. A previous study, flavonoid compound in tea leaves has been proven as antiviral. The development of effective antiviral drugs against COVID-19 remains a challenge for researchers across the world. A previous study investigated the role of the main protease enzyme (Mpro) which is useful in the viral life cycle as a promising drug target. This study aims to know the potential compounds of green tea leaves as a COVID-19 Mpro inhibitor using molecular docking. 12

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Pujiono, Fery EKo, and Tri Ana Mulyati. "Uji Aktivitas Antidiabetes Kokristal Asam Sinamat-Nikotinamide: Study in silico." Journal of Herbal, Clinical and Pharmaceutical Science (HERCLIPS) 5, no. 01 (2023): 26. http://dx.doi.org/10.30587/herclips.v5i01.6243.

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Asam sinamat merupakan senyawa metabolit sekunder yang memiliki aktivitas biologis sebagai antidiabetes. Asam sinamat memiliki kelarutan yang rendah sehingga perlu dikembangkan sebagai kokristal. Disisi lain, efektivitas kokristal asam sinamat terhadap aktivitas antidiabetes belum pernah dilaporkan. Tujuan penelitian ini adalah mengetahui aktivitas asam sinamat dan kokristal asam sinamat – nikotinamida sebagai antidiabetes. Penelitian ini diawali dengan penyiapan ligan dengan Chem3D selanjutnya ligan dan logam tersebut disiapkan untuk penambatan molekular dengan AutoDock Tools. Proses penambat

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