Relevant bibliographies by topics / AutoDockVina

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Academic literature on the topic 'AutoDockVina'

Author: Grafiati
Published: 2 June 2025
Last updated: 19 July 2025

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Journal articles on the topic "AutoDockVina"

1

Joshua Anthony Vomo, Papireddypalli Sushma, Bukke Geethanjali, B Dhanush, and Kanala Somasekhar Reddy. "Swiss Dock 2025: Docking approaches comparison between attracting cavities and autodockvina." World Journal of Biology Pharmacy and Health Sciences 22, no. 2 (2025): 120–25. https://doi.org/10.30574/wjbphs.2025.22.2.0452.

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Molecular docking is a crucial computational tool in drug discovery enabling the prediction of ligand-target interactions and accelerating the screening of potential drug candidates. This study compares twowidely used docking algorithms AutodockVina and Attracting Cavities to evaluate their efficiency, accuracy and applicability in molecular docking studies. AutodockVina is known for its speed and computational efficiency making it suitable for high-throughput screening. In contrast, Attracting Cavities provides more accurate binding predictions particularly for covalent interactions but it requires significantly more computational time. The studies suggest that AutodockVina is preferable for rapid screening whereas Attracting Cavities is advantageous for detailed validation studies. Despite these advancements, molecular docking faces challenges in flexibility modelling, scoring function accuracy and solvation effects. Future directions involve integrating machine learning and quantum chemistry to improve predictive accuracy. This study highlights the importance of selecting docking algorithms based on study-specific requirements for drug discovery.
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2

Mohammed, Z. M., Z. K. Haruna, Z. I. Abdullahi, et al. "In-silico comparative study of three (3) bioactive compounds from methanol extracts of Combretum micranthum leaf, and diazepam with Gabaa receptor molecule." Bayero Journal of Pure and Applied Sciences 12, no. 1 (2020): 235–41. http://dx.doi.org/10.4314/bajopas.v12i1.37s.

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Stress affects monoamine neurotransmitter in the central nervous system such as GABA (a major inhibitory neurotransmitter in the brain). GABAA receptor is hetero-oligomeric Cl-channel that is elective blocked by the alkaloid, bicuculline and modulated by steroids, barbiturates and benzodiazepines. The anticonvulsant activity of Diazepam may be mediated by enhancement of inhibition involving gamma-aminobutyric acid (GABA). Combretum micranthum is one of the maximum effective medicinal plants of therapeutic importance. Thus this study is to examine the effect of Combretum micranthum methanol leaf extract on GABAA Receptor via In-Silico analysis. Combretum micranthum methanol leaf extract was found using GC-MS to contain bioactive compounds (3,5-dichlorophenylhydrazine, guanidine and aminooxyacetic acid) with GABAergic functions. And the popular docking programs PatchDock and AutoDockVina were then used to predict computationally binding modes of these compounds with GABAA receptor. The molecular docking analyses indicated highly and effectively interactions (binding energy in kcal/mol) between GABAA receptor and the Combretum micranthum compounds (ligands): 3,5-dichlorophenylhydrazine (-193.85 and-5.6), guanidine (-87.63 and -3.3) and aminooxyacetic acid (-85.3 and -3.2) for both PatchDock and AutoDock Vina respectively. Results shows that 3,5-dichlorophenylhydrazine has a close binding energy in kcal/mol to that of Diazepam (-200.68 and -6.1 respectively). Findings of the study shows that the interaction between Combretum micranthum compounds (3,5-dichlorophenylhydrazine, guanidine and aminooxyacetic acid) with GABAA receptor can be explore for the development of new therapeutics to manage mental disorders. 
 Keywords: Gamma-aminobutyric acid, Combretum micranthum , AutoDockVina, PatchDock
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3

Jagtap, Vaibhavkumar, Pooja Kakad, Jayprakash Suryawanshi, and Nitinchandra Patil. "Unlocking Novel Therapeutic Avenues: Drug Repurposing and Virtual Screening for Breast Cancer Targeting the Estrogen Receptor." INTERNATIONAL JOURNAL OF PHARMACEUTICAL QUALITY ASSURANCE 15, no. 02 (2024): 815–20. http://dx.doi.org/10.25258/ijpqa.15.2.42.

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This study explores the potential of drug repurposing for breast cancer therapy through virtual screening of Food and Drug Administration (FDA)-approved drugs against breast cancer-related targets. The estrogen receptor alpha ligand-binding domain, a key player in breast cancer progression, served as the primary target for virtual screening. Utilizing the DrugRep Virtual Screening Server and AutoDockVina, several compounds were identified with high binding affinities to the target protein. Notably, estradiol, benzhydrocodone, and ezetimibe emerged as top hits, showcasing diverse physicochemical properties and suggesting novel therapeutic possibilities. The structural fidelity of the estrogen receptor complex was validated through PDB-REDO refinement, enhancing the reliability of the binding interactions predicted. These findings underscore the potential of drug repurposing as a strategy for uncovering new therapeutic options in breast cancer treatment, warranting further biological validation and clinical exploration
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4

Aliyah, Alma Nuril, Fauz Aulia El Maghfiroh та Fathia Faza Rahmadanita. "in Silico Prediction of Caesalpinia sappan L. Secondary Metabolites towards PPARγ". Proceeding Annual Symposium on Hajj and Umrah Medicine 1 (5 грудня 2022): 42. https://doi.org/10.18860/anshar.v1i0.2134.

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Chemotherapy can cause mitochondrial dysfunction and oxidative stress that induces Chemotherapy-induced Peripheral Neurotherapy (CIPN) condition. Inhibition of pro-inflammatory transcription factors by PPARγ agonist can be used to develop CIPN treatment. To find potential compounds from plants, this study conducted an in silico study of the secondary metabolites of Caesalpinia sappan L. In this study, we conducted a molecular docking study of 27 secondary metabolites of Caesalpinia sappan L. using an in silico approach targeting PPARγ (PDB ID: 2PRG) using AutoDockVina software. ADMET characteristics were predicted using the SwissADME and pkCSM Online Tool. The results showed that metabolites from Caesalpinia sappan L. with the strongest affinity for PPARγ were Phanginin D, Phanginin E, Phanginin H, Phanginin A, Phanginin G, Phanginin B, Neosappanone A, and 8-Methoxybonducellin, compared to the native ligand. Therefore, that metabolites potentially to be developed as a treatment for CIPN.
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5

Sousa, Glaydiane Alves de, Ivis Vinicius de Oliveira Martins, Vinícius Duarte Pimentel, and Joubert Aires Sousa. "Análise in silico da farmacodinâmica, farmacocinética e toxicidade de dois compostos isolados da Actinidia deliciosa para investigação do seu potencial anti-hiperlipêmico." Research, Society and Development 9, no. 7 (2020): e790974679. http://dx.doi.org/10.33448/rsd-v9i7.4679.

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A presente pesquisa visou avaliar in silico a farmacodinâmica, farmacocinética e toxicidade dos ácidos siríngico e ursólico isolados da Actinidia deliciosa e analisar o mecanismo que fundamente a sua atuação na redução do colesterol comparando-os com o fármaco sinvastatina. Foi utilizado o servidor online PreADME para a avaliação do perfil farmacocinético e toxicológico por meio da estrutura-atividade molecular e o software AutodockVina para o estudo da farmacodinâmica e potencial farmacológico das interações moleculares. Os dados ADME obtidos para os ácidos siríngico e ursólico foram semelhantes aos da sinvastatina, na análise do docking molecular foi evidenciado que os resultados foram aproximados entre as moléculas testadas, contudo o ácido ursólico se sobrepôs com maior estabilidade de interação com o alvo biológico quando comparado a sinvastatina. Foi possível observar a partir dos resultados que os compostos avaliados são qualificados a posteriores ensaios in vitro e in vivo para um estudo mais aprofundado de sua ação anti-hiperlipêmica.
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6

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 for these ligands, but Vina performed best in terms of precision and docking success rates. The results provide important guidance for the selection of appropriate support tools for screening potential HIV-1 protease inhibitors in treating HIV/AIDS. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium provided the original work is properly cited.
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7

Sharma, Abhishek Shankar, Salahuddin Salahuddin, Kavita Rana, et al. "Synthesis, anticonvulsant potential, and molecular docking studies of Schiff bases bearing 2', 6-dichloro-2,3'-biquinoline." INDIAN JOURNAL OF HETEROCYCLIC CHEMISTRY 35, no. 01 (2025): 119. https://doi.org/10.59467/ijhc.2025.35.119.

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In the present manuscript, a series of new 2',6-dichloro-N'-(substituted-benzylidene)-[2,3'-biquinoline]-4- carbohydrazides (6a-l; Schiff bases) has been synthesized by the reaction of 2',6-dichloro-[2,3']biquinolinyl-4-carboxylic acid hydrazide (5) with substituted benzaldehydes. All compounds have been screened for anticonvulsant potential by using the subcutaneous pentylenetetrazole model. From the entire series the compounds 6a, 6c, and 6e showed protection against convulsions at the dose concentration of 30 mg/kg body weight in correlation with conventional drug (phenytoin). The molecules have shown effective binding affinity ranges from -8.5 kcaL/moL to -9.8 kcaL/moL. The most suitable orientation and binding interactions were observed with compounds 6b, 6c, 6h, and 6i. The binding energies of the compounds 6b, 6c, 6h, and 6i were found to be -9.7, -9.8, -9.7, -9.8 KcaL/moL by Autodock-w and -9.7, -9.8, -9.8 and -9.7 KcaL/moL, respectively, by autodockvina.. KEYWORDS :Epilepsy, Antiepileptic potential, Schiff base, Bis quinoline, Subcutaneous pentylene tetrazole.
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8

Ritik R. Jamgade, Ritik R. Jamgade, Dr Dinesh R. Chaple Dr. Dinesh R. Chaple, Rida K. Saiyyad Rida K. Saiyyad, Prerna P. Bhange Prerna P. Bhange, Nandani K. Sonwane Nandani K. Sonwane, and Shivani P. Wadichar Shivani P. Wadichar. "Molecular Docking and ADME-Based Prioritization of 20 Quinazolinone Scaffolds for Anticonvulsant Potential." International Journal of Pharmaceutical Research and Applications 10, no. 3 (2025): 2046–63. https://doi.org/10.35629/4494-100320462063.

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Quinazolinone derivatives have attracted significant attention for their broad pharmacological potential, particularly in the treatment of central nervous system (CNS) disorders such as epilepsy. In the present study, a series of twenty novel quinazolinone derivatives were designed and evaluated for their potential anticonvulsant activity through molecular docking studies. The compounds were docked into the active site of the GABAAreceptor, a wellestablished target for antiepileptic drugs, using its crystallographic structure (PDB ID: 4COF). Molecular docking was carried out using AutoDockVina, and binding affinities were compared to standard antiepileptic agents. Several compounds demonstrated high binding affinity toward the receptor, with key hydrogen bonding and hydrophobic interactions involving critical amino acid residues such as TYR157, THR202, and PHE77. The top-performing derivative exhibited a binding energy of –9.3 kcal/mol, suggesting strong interaction and potential modulation of GABAergic signaling. These results support the potential of quinazolinone scaffolds as promising leads for the development of new anticonvulsant agents, and warrant further in vitro and in vivo validation.
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9

Alamri, Abdulhakeem S., Majid Alhomrani, Walaa F. Alsanie та ін. "Spectroscopic and Molecular Docking Analysis of π-Acceptor Complexes with the Drug Barbital". Applied Sciences 12, № 19 (2022): 10130. http://dx.doi.org/10.3390/app121910130.

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The drug barbital (Bar) has a strong sedative–hypnotic effect. The intermolecular charge transfer compounds associated with the chemical reactions between Bar and some π acceptors, such as 2,6-dibromoquinone-4-chloroimide (DBQ), tetracyanoquinodimethane (TCNQ), chloranil (CHL), and chloranilic acid (CLA), have been synthesized and isolated in solid state. The synthesized products have the molecular formulas (Bar–DBQ), (Bar–TCNQ), (Bar–CHL), and (Bar–CLA) with 1:1 stoichiometry based on Raman, IR, TG, 1H NMR, XRD, SEM, and UV-visible analysis techniques. Additionally, the comparative analysis of molecular docking between the donor reactant moiety, Bar, and its four CT complexes was conducted using two neurotransmitter receptors (dopamine and serotonin). The docking results obtained from AutoDockVina software were investigated by a molecular dynamics simulation technique with 100ns run. The molecular mechanisms behind receptor–ligand interactions were also looked into. The DFT computations were conducted using theory at the B3LYP/6-311G++ level. In addition, the HOMO LUMO electronic energy gap and the CT complex’s optimal geometry and molecule electrostatic potential were examined.
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10

Annastasia ERAZUA, Ehimen, and Babatunde Benjamin ADELEKE. "DFT and Molecular Docking Investigation of Potential Anticancer Properties of Some Flavonoids." Journal of Pure and Applied Chemistry Research 8, no. 3 (2019): 225–31. http://dx.doi.org/10.21776/ub.jpacr.2019.008.03.485.

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There is a continuous need to discover and obtain more efficient drug-like molecule to suppress cancer in human being. Recently researchers are using molecular docking technique to improve the understanding of the interaction between drug and receptor, in other to obtain novel drugs for more efficient usage. Anticancer activities of some selected flavonoids were studied using quantum chemical method through Density Functional Theory (DFT) and molecular docking approach. These Flavoniods were docked against breast cancer cell line (3s7s) using Autodock tool, AutoDockVina as docking tools and Biovia Discovery Studio 2017 for post docking analysis. The binding affinity obtained was used to correlate the inhibitory activity of these flavoniods with their calculated molecular descriptors. The obtained binding energy showed that quercetin has the highest inhibition efficiency hence it has the highest ability to inhibit 3s7s than other studied compounds. It was observed that some molecular descriptor such as band gap, dipole moment, logP and EHOMO, were significant to the inhibiting ability of quercetin in the active site of the protein.
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