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Journal articles on the topic 'DOCKING SCORE'

Author: Grafiati

Published: 11 September 2023

Last updated: 25 July 2025

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1

Kumar, Harsh, Aastha Sharma, Davinder Kumar, Minakshi Gupta Marwaha, and Rakesh Kumar Marwaha. "3-(Substituted Aryl/alkyl)-5-((E)-4-((E)-(Substituted Aryl/alkyl)methyl)benzylidene) thiazolidin-2,4-dione Molecules: Design, ADME Studies and Molecular Docking Analysis as Potential Antimicrobial and Antiproliferative Agents." Asian Journal of Chemistry 34, no. 9 (2022): 2393–405. http://dx.doi.org/10.14233/ajchem.2022.23927.

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A library comprising of 60 synthesizable compounds from three different series having 20 compounds in each series of 3-(furan-2-carbonyl)-5-((E)-4-((E)-(substituted aryl/ alkyl)methyl)benzylidene)thiazolidine-2,4-dione (FC-1 to FC-20), 3-(butyl)-5-((E)-4-((E)-(substituted aryl/alkyl)methyl)benzylidene)thiazolidine-2,4-dione (NB-1 to NB-20) and 3-(allyl)-5-((E)-4-((E)- (substituted aryl/alkyl)methyl)benzylidene)thiazolidine-2,4-dione (NA-1 to NA-20) was designed and screened for antimicrobial and anticancer potential by molecular docking studies using S. aureus GyrB ATPase (PDB code: 3U2D) and

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G., Lalitha, Sneha Suresh, and Vijay Rajendran. "IN SILICO BASED SCREENING EMPLOYED TO ASSESS THE ACTIVITY OF PHYTOCHEMICAL, SYNTHETIC AND MARINE COMPOUNDS ON THE SARSCOV-2 MAIN PROTEASE." INDIAN DRUGS 61, no. 07 (2024): 23–33. http://dx.doi.org/10.53879/id.61.07.14596.

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Our study focuses on screening ligands against the target 6Y2E using the iGemDock docking program, encompassing phytochemical, synthetic and marine sources, suggesting suitability for oral use against SARS-CoV-2 Main protease. Docking process involves iGemDock program for assessment, Argus Labs, for binding energy determination, Swiss ADME for evaluating pharmacological properties, and Chimera for visualizing interactions. Docking score gauges how effectively a ligand inhibits SARSCoV-2 Mpro, with compounds ranked based on their docking scores. Rosmarinic acid, a phytochemical compound, achiev

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Pratama, Mohammad Rizki Fadhil, Hadi Poerwono, and Siswandono Siswodihardjo. "Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions." Indonesian Journal of Biotechnology 26, no. 1 (2021): 54. http://dx.doi.org/10.22146/ijbiotech.62194.

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Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained be

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4

Scobie, D. R., D. O'Connell, C. A. Morris, and S. M. Hickey. "A preliminary genetic analysis of breech and tail traits with the aim of improving the welfare of sheep." Australian Journal of Agricultural Research 58, no. 2 (2007): 161. http://dx.doi.org/10.1071/ar05444.

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The area of naturally bare skin around the perineum was scored at weaning in lambs (n = 2152) from a composite flock of New Zealand crossbred sheep. Breech bareness was scored on a range from 1, where wool was growing right to the edges of the anus, to 5, where a large bare area surrounded the perineum. Bareness on the under surface of the tail was measured on a linear scale at tail docking. Dag score (degree of breech soiling) was recorded at weaning, on a scale of 0–5, where an increasing score indicated more dags. Dag score was taken as a measure of the risk of flystrike in the breech. Fema

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5

Mohanasundaram, Sugumar, Porkodi Karthikeyan, Venkatesan Sampath, et al. "Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2." Cellular Microbiology 2024 (January 16, 2024): 1–19. http://dx.doi.org/10.1155/2024/6647757.

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Considering natural compounds for the antiviral effect is another opportunity for exploring novel drug candidates for severe acute respiratory syndrome coronavirus 2. The selected natural compounds were interacted using a molecular docking approach. The 3D structures of the main protease and papain-like protease were used for the virtual screening to detect the potent inhibitor against SARS-CoV-2. The top-scored compounds were further analyzed for absorption, digestion, metabolism, excretion, and toxicity properties and density functional theory analysis. Our results indicated that glycyrrhizi

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6

Feher, Miklos, and Christopher I. Williams. "Reducing Docking Score Variations Arising from Input Differences." Journal of Chemical Information and Modeling 50, no. 9 (2010): 1549–60. http://dx.doi.org/10.1021/ci100204x.

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7

Choi, Jieun, and Juyong Lee. "V-Dock: Fast Generation of Novel Drug-like Molecules Using Machine-Learning-Based Docking Score and Molecular Optimization." International Journal of Molecular Sciences 22, no. 21 (2021): 11635. http://dx.doi.org/10.3390/ijms222111635.

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We propose a computational workflow to design novel drug-like molecules by combining the global optimization of molecular properties and protein-ligand docking with machine learning. However, most existing methods depend heavily on experimental data, and many targets do not have sufficient data to train reliable activity prediction models. To overcome this limitation, protein-ligand docking calculations must be performed using the limited data available. Such docking calculations during molecular generation require considerable computational time, preventing extensive exploration of the chemic

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Srivastava, Snigdha, Reema Sinha, Pallavi Manish Lavhale, and Rajan Kumar Kurmi. "MOLECULAR DOCKING PREDICTION OF CARVONE TOWARDS GABA-ATASE AND SODIUM CHANNEL." Journal of Applied Pharmaceutical Sciences and Research 6, no. 2 (2023): 16–18. http://dx.doi.org/10.31069/japsr.v6i2.03.

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Aim: Modern tool designs frequently employ molecular docking to anticipate small molecules’ binding orientation and better comprehend drug-receptor interactions. Carvone’s molecular docking analysis against sodium channels and GABA-AT is part of this research investigation. Introduction: Carvone’s molecular docking analysis against sodium channels and GABA-AT is part of this research investigation. The biological significance of carvone has been demonstrated to include anti-epileptic, anti-fungal, anti-inflammatory, anti-cancer, and antioxidant effects. In modern drug design, molecular d

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9

Rizma, Baiq Ressa Puspita, Agus Dwi Ananto, and Anggit Listyacahyani Sunarwidhi. "The Study of Potential Antiviral Compounds from Indonesian Medicinal Plants as Anti-COVID-19 with Molecular Docking Approach." Journal of Molecular Docking 1, no. 1 (2021): 32–39. http://dx.doi.org/10.33084/jmd.v1i1.2307.

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Corona Virus Disease 2019 (COVID-19) is a new strain of coronavirus called SARS-CoV-2, which was identified in Wuhan, China, in December 2019. The rapid transmission of COVID-19 from human to human forced researchers to find a potent drug by setting aside the time-consuming traditional method in drug development. The molecular docking approach is one a reliable method to screening compound from chemical drug or by finding a compound from Indonesian herbal plants. The present study aimed to assess the potency of compounds from five medicinal plants as potential inhibitors of PLpro and 3CLpro fr

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10

Hussain, Rafaqat, Wajid Rehman, Shoaib Khan, et al. "Imidazopyridine-Based Thiazole Derivatives as Potential Antidiabetic Agents: Synthesis, In Vitro Bioactivity, and In Silico Molecular Modeling Approach." Pharmaceuticals 16, no. 9 (2023): 1288. http://dx.doi.org/10.3390/ph16091288.

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A new series of thiazole derivatives (4a-p) incorporating imidazopyridine moiety was synthesized and assessed for their in vitro potential α-glucosidase potency using acarbose as a reference drug. The obtained results suggested that compounds 4a (docking score = −13.45), 4g (docking score = −12.87), 4o (docking score = −12.15), and 4p (docking score = −11.25) remarkably showed superior activity against the targeted α-glucosidase enzyme, with IC50 values of 5.57 ± 3.45, 8.85 ± 2.18, 7.16 ± 1.40, and 10.48 ± 2.20, respectively. Upon further investigation of the binding mode of the interactions b

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Navhaya, Liberty T., Thabe M. Matsebatlela, Mokgerwa Z. Monama, and Xolani H. Makhoba. "In Silico Discovery and Evaluation of Inhibitors of the SARS-CoV-2 Spike Protein–HSPA8 Complex Towards Developing COVID-19 Therapeutic Drugs." Viruses 16, no. 11 (2024): 1726. http://dx.doi.org/10.3390/v16111726.

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The SARS-CoV-2 spike protein is pivotal in the COVID-19 virus’s life cycle, facilitating viral attachment to host cells. It is believed that targeting this viral protein could be key to developing effective COVID-19 prophylactics. Using in silico techniques, this study sought to virtually screen for compounds from the literature that strongly bind and disrupt the stability of the HSPA8–spike protein complex. To evaluate the interactions between the individual proteins and the protein complex attained from protein–protein docking using BioLuminate, molecular docking was performed using the Maes

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Xu, Siqi, Li Wang, and Xianchao Pan. "An evaluation of combined strategies for improving the performance of molecular docking." Journal of Bioinformatics and Computational Biology 19, no. 02 (2021): 2150003. http://dx.doi.org/10.1142/s0219720021500037.

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Molecular docking is a fast and efficient computational method for the prediction of the binding mode and binding affinity between a ligand and a target protein at the atomic level. However, the performance of current docking programs is less than satisfactory. Herein, with a focus on free programs and scoring functions, the performances of LeDock and three standalone scoring functions were tested by 195 high-quality protein–ligand complexes. Results showed that the success rate for the best pose of the free available docking program LeDock achieved 89.20%, indicative of a strong sampling powe

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13

Yadav, Reena, and Jitender K. Malik. "In –Silico Approach for Assessment of Antimicrobial Potential of some Pyrazolidine-3, 5-Dione Derivatives." Global Academic Journal of Pharmacy and Drug Research 4, no. 3 (2022): 51–58. http://dx.doi.org/10.36348/gajpdr.2022.v04i03.001.

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Background: Resistance to antibacterial drugs is a trouble in the worldwide public health that must be conquered immediately by finding new antibacterial drugs.Pyrazolidine-3, 5-dione derivatives of heterocyclic compounds were used as active agents against pathogenic microorganisms. This study has been carried out to rationally design three synthesized derivatives was assayed for antimicrobial potential by using in-silico molecular docking approach. Methods: Molecular docking of Isoleucyl-transfer RNA (tRNA) synthetase (IleRS) with three Pyrazolidine-3, 5-dione synthesized derivatives was carr

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14

Mali, Pooja, Shourya Pratap, Raghvendra S. Badhauria, and Himanshu Gurjar. "DOCKING STUDIES OF AMINOHYDANTOIN DERIVATIVES AS ANTIMALARIAL AGENTS." Journal of Drug Delivery and Therapeutics 8, no. 5-s (2018): 322–26. http://dx.doi.org/10.22270/jddt.v8i5-s.1983.

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Objective: Docking studies of aminohydantoin derivatives as antimalarial agents. A novel derivative of aminohydantoins was selected from the literature. Method: in-silco studies using docking methodology. The compounds were sketched and energy minimized using Chem draw ultra and Chem 3D ultra respectively. Further, the compounds were docked into Plasmodium falciparum transferase inhibitor (3L7) using Molegro Virtual Platform. Twenty eight compounds were docked into the active site of Pf-lactate dehydrogenase cavity and all of them found to have similar binding interactions of a co-crystalized

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15

Rizma, Baiq Ressa Puspita, Yek Zen Mubarok, Dian Fathita Dwi Lestari, and Agus Dwi Ananto. "Molecular Study of Antiviral Compound of Indonesian Herbal Medicine as 3CLpro and PLpro Inhibitor in SARS-COV-2." Acta Chimica Asiana 4, no. 2 (2021): 127–34. http://dx.doi.org/10.29303/aca.v4i2.74.

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Rapid transmission of COVID-19 disease and the fatal effects of the disease lead researchers to use various way to find potential anti-COVID-19 compounds, including using modern approaches. Molecular docking is one of the methods that can be used to analyse antiviral compounds and its molecular target from Indonesian herbs that are believed to have properties as anti-COVID-19. This study aims to analyse antiviral compounds from 5 herbs that have the potential as inhibitors of PLpro and 3CLpro, which both are a non-structural protein in SARS-CoV-2 by molecular docking approach using PLANTS. Rem

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16

Kim, Stephanie S., Melanie L. Aprahamian, and Steffen Lindert. "Improving inverse docking target identification with Z ‐score selection." Chemical Biology & Drug Design 93, no. 6 (2019): 1105–16. http://dx.doi.org/10.1111/cbdd.13453.

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17

Verma, Mohit, Preeti Jyoti, Devkant Sharma, and Anurag Bhargava. "Docking Studies of Histone Deacetylases Inhibitors." Asian Pacific Journal of Health Sciences 9, no. 4 (2022): 13–18. http://dx.doi.org/10.21276/apjhs.2022.9.4.03.

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To augment hits from a high through put screening, a docking study on N-hydroxy phenyl acrylamides and N-hydroxy pyridine-derivatives was performed as histone deacetylases inhibitors. Twenty-nine ligands were docked inside the ligand-binding domain of protein data bank PDB ID: 1C3S utilizing Molegro version 4.02. All 29 compounds, compounds were found to embed in the hydrophobic pocket by forming hydrogen bonds. Almost all compounds were found to have highest MolDock score in comparison to reference or coexisting ligand in protein. The compounds that had highest MolDock score are generally con

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18

Rizqillah, Raihan Kenji, Jaka Fajar Fatriansyah, Fadilah, et al. "In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease." BIO Web of Conferences 41 (2021): 07002. http://dx.doi.org/10.1051/bioconf/20214107002.

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In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone have comparable inhibition activ

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19

Raj, Priya Durai, Palagati Rohith Kumar Reddy, Palaniyandi Thiruvanavukkarasu, Sindhu Rajesh, and Rajeswary Hari. "Anticancer Activity of Phyto Ligands from Carica papaya Leaves by Suppression of PI3CKA and BCL2 Proteins- An insilico Approach." Biomedical and Pharmacology Journal 15, no. 3 (2022): 1289–98. http://dx.doi.org/10.13005/bpj/2466.

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The plant derived compounds possess several medicinal property including anticancer activities. In the present investigation molecular docking analysis was performed to identify a suitable antagonistic ligand from the phyto ligands of Carica pappya leaves which can inhibit the tumor progressive proteins PIK3CA, BCL 2. The molecular Docking analysis was performed using Autodock 4.2. The protein PIK3CA, BCL 2 structures were retrieved from PDB, and by GC-MS analysis the phyto molecules were identified. The ligand chemical structures were drawn using Chem sketch. The enzyme and ligand interaction

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Dilek, Ömer, Tolga Acar Yeşil, and Tahir Tilki. "A New Candidate for the Treatment of Alzheimer's Disease; Synthesis, Characterization, Investigation of Drug Properties with In Silico Methods." Cumhuriyet Science Journal 46, no. 1 (2025): 62–72. https://doi.org/10.17776/csj.1487341.

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Brain disorder-caused mortality has emerged as the second of all diseases worldwide in the 21st century. Alzheimer’s Disease (AD) is the most common disease that takes place among brain disorders according to statistics. Therefore, in this study, potential new drug candidate for AD (2-amino-N'-benzylidene-4-(trifluoromethyl)benzohydrazide, ABTH) was synthesized, starting from -CF3 and -NO2 containing carboxylic acid. The structure of ABTH was elucidated using 1H, 13C-APT NMR, FTIR, and Mass analyses. ADMEt properties were calculated and from the ADMEt results, it was observed that the ABTH cro

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Angelova, Maria, Petko Alov, Ivanka Tsakovska, et al. "Pairwise Performance Comparison of Docking Scoring Functions: Computational Approach Using InterCriteria Analysis." Molecules 30, no. 13 (2025): 2777. https://doi.org/10.3390/molecules30132777.

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Scoring functions are key elements in docking protocols as they approximate the binding affinity of a ligand (usually a small bioactive molecule) by calculating its interaction energy with a biomacromolecule (usually a protein). In this study, we present a pairwise comparison of scoring functions applying a multi-criterion decision-making approach based on InterCriteria analysis (ICrA). As criteria, the five scoring functions implemented in MOE (Molecular Operating Environment) software were selected, and their performance on a set of protein–ligand complexes from the PDBbind database was comp

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Saputri, Dwi, Triana Kusumaningtyas, Prismo Setiadi, and Rifki Febriansah. "Investigation of Moringa Leaf Compounds as Colon Anticancer Agents Using Bioinformatics and Molecular Docking Methods." Proceedings University of Muhammadiyah Yogyakarta Undergraduate Conference 2, no. 2 (2022): 24–27. http://dx.doi.org/10.18196/umygrace.v2i2.421.

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Introduction - Colon cancer is a disease that has a high mortality rate. Cancer treatments such as chemotherapy can cause severe side effects. So, it is necessary to do research on herbal plants to minimize these side effects. The bioactive compounds in Moringa leaves (Moringa oleifera L.) are known to have antioxidant and anticancer activity, so they have the potential to be used as cancer treatment. Purpose – . This study aims to determine the potential of Moringa leaves as an anticancer agent in silico. Methodology/Approach – The in silico test used is STITCH-STRING bioinformatics and

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Mateev, Emilio Viktorov, Iva Valkova, Maya Georgieva, and Alexander Zlatkov. "Suitable Docking Protocol for the Design of Novel Coumarin Derivatives with Selective MAO-B Effects." Journal of Molecular Docking 1, no. 1 (2021): 40–47. http://dx.doi.org/10.33084/jmd.v1i1.2357.

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Recently, the application of molecular docking is drastically increasing due to the rapid growth of resolved crystallographic receptors with co-crystallized ligands. However, the inability of docking softwares to correctly score the occurred interactions between ligands and receptors is still a relevant issue. This study examined the Pearson’s correlation coefficient between the experimental monoamine oxidase-B (MAO-B) inhibitory activity of 44 novel coumarins and the obtained GOLD 5.3 docking scores. Subsequently, optimization of the docking protocol was carried out to achieve the best possib

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Narulita, Erlia, Annisyah Nurmitha Oktarina, Rina B. Opulencia, Agung Haris Widianto, Riska Ayu Febrianti, and Hardian Susilo Addy. "CRISPR-Cas Single-Guide RNA Construction for Tail Fiber Gene Gp0047 of Salmonella Phage SSE-121." Turkish Computational and Theoretical Chemistry 9, no. 3 (2024): 25–37. https://doi.org/10.33435/tcandtc.1531868.

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In this study, we conducted an in-silico study of single guide RNA (sgRNA) construction as the initial stage of CRISPR-Cas9-based genome editing on Salmonella bacteriophage SSE-121 to broaden its host range. The results of the study discovered 188 sgRNA candidates using CHOPCHOP prediction. All selected candidates were docked using free website-based docking tools HNADOCK, therefore the top seven candidates of sgRNAs were docked using HDOCK with the Cas9 protein. The molecular dynamics simulation of the most optimum sgRNA-Cas9 protein (docking score -387.43) and sgRNA-Cas9-DNA (docking score -

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Santoso, Broto. "EXPLORING 3D MOLECULAR STUDIES OF DIKETOPIPERAZINE ANALOGUES ON Staphylococcus aureus DEHYDROSQUALENE SYNTHASE USING GLIDE-XP." Pharmacon: Jurnal Farmasi Indonesia 13, no. 2 (2012): 77–86. http://dx.doi.org/10.23917/pharmacon.v13i2.14.

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There is a strong correlation between 3D molecular docking result with dehydrosqualene synthase protein and antibacterial activity against Staphylococcus aureus (S. aureus) of the pyrazoline analogues. The enzyme has been known as important protein for the synthesis of staphyloxanthin in S. aureus. Diketopiperazine analogues have similar structure to pyrazoline. Glide-XP, Schrodinger application that seeks for molecular docking screening between ligand and protein target is designed for speed, efficiency, and accuracy to conduct discovery efforts. The research report the three-dimension molecu

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Pamungkas, Tri Setyo, and Rosario Trijuliamos Manalu. "STUDI IN SILICO SENYAWA AKTIF ASAM JAWA (Tamarindus indica L.) SEBAGAI ANTIDIABETES MELALUI INHIBISI PROTEIN TYROSINE PHOSPHATASE." Jurnal Ilmiah Ibnu Sina (JIIS): Ilmu Farmasi dan Kesehatan 8, no. 1 (2023): 134–44. http://dx.doi.org/10.36387/jiis.v8i1.1282.

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Tamarind leaves (Tamarindus indica L.) are widely cultivated in tropical countries, including Indonesia. Empirically, tamarind leaves are known to have anti-diabetic properties. In this study, an in-silico method was used to test the active compounds found in tamarind leaves (Tamarindus indica L.) as anti-diabetic agents through docking score analysis. The target protein used was Protein Tyrosine Phosphatase (5JNT) which is related to insulin resistance. Glimepiride and native ligand 5JNT were used as reference ligands, while the active compounds of tamarind leaves (Tamarindus indica L.) were

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Zeb, Muhammad Aurang, Taj Ur Rahman, Muhammad Sajid, et al. "GC-MS Analysis and In Silico Approaches of Indigofera heterantha Root Oil Chemical Constituents." Compounds 1, no. 3 (2021): 116–24. http://dx.doi.org/10.3390/compounds1030010.

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The phytochemical investigation on Indigofera heterantha root oil resulted in the identification of 121 phytochemicals using GC-MS analysis. These phytochemicals were docked against alpha-amylase, alpha-glucosidase enzymes. The docking results suggested that Hexacosyl acetate (121) possess alpha-amylase inhibitory potential with a docking score of −8.2944994 and the interaction with alpha-glucosidase enzyme was −9.73762512, followed by 9, 12, 15-Octadecatrienoic acid, 2, 3-dihydroxypropyl ester, (Z, Z, Z)-(83) with a docking score of −9.59869957, showed outstanding results in all the stages of

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Rabar, Denis, Danijela Rabar, and Duško Pavletić. "Two-Step Manufacturing Process Measurement Model Using Qualitative and Quantitative Data—A Case of Newbuilding Dry-Docking." Journal of Marine Science and Engineering 9, no. 5 (2021): 464. http://dx.doi.org/10.3390/jmse9050464.

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Newbuilding dry-docking is a part of the shipbuilding manufacturing process, common for vessels built on slipways. The subject of this research is steel-built vessels intended for non-restricted sea-going navigation. Based on former experience, the necessity of the dry-docking projects measurement has been noted as a managerial tool for performance estimation and project comparison. The dry-docking project is a complex task which includes the first self-propelled sea passage and the transfer of the manufacturing process to a remote place. The dry-docking result is a surveyed and coated vessel

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Bajusz, Dávid, Anita Rácz, and Károly Héberger. "Comparison of Data Fusion Methods as Consensus Scores for Ensemble Docking." Molecules 24, no. 15 (2019): 2690. http://dx.doi.org/10.3390/molecules24152690.

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Ensemble docking is a widely applied concept in structure-based virtual screening—to at least partly account for protein flexibility—usually granting a significant performance gain at a modest cost of speed. From the individual, single-structure docking scores, a consensus score needs to be produced by data fusion: this is usually done by taking the best docking score from the available pool (in most cases— and in this study as well—this is the minimum score). Nonetheless, there are a number of other fusion rules that can be applied. We report here the results of a detailed statistical compari

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Saini, Mohit, and Jitender K. Malik. "In-Silico Validation of Glycyrrhizin against Proinflammatory Mediator COX-2: Anti-Proliferative Potential." South Asian Research Journal of Pharmaceutical Sciences 5, no. 05 (2023): 206–12. http://dx.doi.org/10.36346/sarjps.2023.v05i05.004.

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Background: Licorice's scientific name is Glycyrrhiza glabra. It is a well-known medicinal plant that grows in numerous locations throughout the world. It is one of the most ancient and widely utilised plants and has been used for a very long period in both western and eastern nations. The primary source of the triterpenoid saponin, glycyrrhizic acid (also known as glycyrrhizin), which is a sweeter component and around 50 times sweeter than sugar, was the Glycyrrhiza glabra (Fabaceae) root. Glycyrrhetinic acid has been found as the chemical constituent of glycyrrhizin. Aim: The current work so

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Ciccotti, Michael C., Austin M. Looney, Emma E. Johnson, et al. "A Prospective, Randomized Trial of the Modified Jobe Versus Docking Techniques With Gracilis Autograft for Ulnar Collateral Ligament Reconstruction in the Elbow." American Journal of Sports Medicine 53, no. 2 (2025): 447–62. https://doi.org/10.1177/03635465241305741.

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Background: Ulnar collateral ligament (UCL)reconstruction (UCLR) has transformed UCL injury from career-ending to career-interruptive. The most common surgical techniques are the modified Jobe and docking techniques. Purpose/Hypothesis: The purpose of this study was to perform a prospective, randomized comparison of the modified Jobe versus docking techniques in overhead athletes with respect to patient-reported outcomes (PROs), self-reported baseball-specific metrics, imaging, and complications. It was hypothesized that there would be no significant differences between techniques. Study Desig

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Karnan, R., M. Sukumaran, and S. Velavan. "Correlation between Molecular Docking Score and Ligand Molar Mass: Statistical Approach." UTTAR PRADESH JOURNAL OF ZOOLOGY 44, no. 19 (2023): 98–105. http://dx.doi.org/10.56557/upjoz/2023/v44i193623.

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In recent days, pharmacology researchers have studied secondary metabolic compounds because they are naturally produced by plants, bacteria, fungi, and marine sponges, leading to increased worldwide use of the computational technique of molecular modelling approaches to drug discovery. Flavonoids, which belong to secondary metabolic compounds, play a role in biological activity. In the present study, the flavonoids subclass of secondary metabolic compounds molecular docking binding energy was dependent on the compound's molecular weight on binding interaction with antioxidant proteins using th

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Maurya, Anil, and Jitender K. Malik. "Anti-Inflammatory Potential and Underlying Mechanistic of Phenolic Component from Ziziphus jujuba Fruit: A Molecular Docking Validation." EAS Journal of Pharmacy and Pharmacology 5, no. 03 (2023): 43–48. http://dx.doi.org/10.36349/easjpp.2023.v05i03.001.

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The nutritious jujube fruit (Ziziphus jujube Mill.) is a member of the Rhamnaceous family and grows mainly in inland areas of Europe, southern and eastern Asia, Australia and especially northern China. Jujubes have a long history as fruit and medicinal. The main bioactive components are vitamin C, phenols, flavonoids, triterpenoids and polysaccharides. Chlorogenic acid (5-O-caffeoylquinic acid) is a phenolic compound of the hydroxycinnamic acid family found in the hydroethanolic fruit extract of Z.jujuba. This polyphenol has many health-enhancing properties, most of which are relevant for the

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Mourya, Brijendra, and Niyati Shrivastava. "Mechanistic Insights an Anti-Inflammatory Potential of Quercetin by Molecular Docking." Global Academic Journal of Pharmacy and Drug Research 4, no. 3 (2022): 59–65. http://dx.doi.org/10.36348/gajpdr.2022.v04i03.002.

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Background: Inflammation is a biological response to a series of chemical reactions whose major function is protection from infection and the resolution of tissue damage caused by injury. There are several mediators released during the process of inflammation. Flavonoids are universal in photosynthesizing cells and are often found in vegetables, fruit, nuts, seeds, stems, tea, flowers, honey and wine preparations. This class of natural products is becoming the subject of anti-infective research, and many groups have isolated and identified the structures of flavonoids possessing, antiviral, an

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Hadi, samsul, and Kunti Nastiti. "PENDEKATAN KOMPUTASI UNTUK MENGATASI MALARIA DARI Coscinium fenestratum." Jurnal Insan Farmasi Indonesia 6, no. 2 (2023): 280–88. http://dx.doi.org/10.36387/jifi.v6i2.1412.

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Malaria is a disease with signs of fever and is caused by Plasmodium. One way to inhibit the growth of plasmodium is using Dihydroorotate dehydrogenase inhibitors. The method used in this study was docking with laptop aspire ES 14 equipment and PLANTS software for docking and the Discovery Studio for visualization and the materials used were compounds contained in C. fenestratum. This research was carried out using protein code 6VTY which removed water molecules and ligands that were not linked to the active site, and continued with the docking of the compounds contained in C. fenestratum. The

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Pentu, Narendra, Ajitha Azhakesan, and Pasupuleti Kishore Kumar. "Insilico molecular docking and ADME/T studies of flavonol compounds against selected proteins involved in inflammation mechanism." Journal of Applied Pharmaceutical Research 13, no. 1 (2025): 95–111. https://doi.org/10.69857/joapr.v13i1.706.

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Background: Using computational tools in drug discovery advanced the research in identifying new drug candidates for the benefit of the pharmaceutical industry and assessing the safety and pharmacokinetic profiles of phytochemicals. Understanding the inflammatory mechanism is not possible, but inflammatory signal transduction by cytokines can be mitigated by using the flavonoid class of drugs like flavonols. Methodology: A molecular docking study of flavonol compounds with proteins linked with inflammation was carried out using the AutodockVina program. SwissADME and pkCSM modules were used to

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Sarika, Patil* Sanskruti More Monali Thorat Anuja Masule. "Molecular Docking, Pharmacophore Mapping And Virtual Screening Of Potent Human P-Glycoprotein Inhibitors." International Journal of Pharmaceutical Sciences 2, no. 10 (2024): 1358–72. https://doi.org/10.5281/zenodo.13895988.

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Multidrug resistance (MDR) is a prevalent issue when treating cancer with chemotherapy. For development of inhibitors to combat multidrug resistance in cancer cells, P-glycoprotein (P-gp) serves as therapeutic target. In the quest of new potent human p-glycoprotein modulators, series of compounds were screened through process of molecular docking followed by pharmacophore mapping and virtual screening as a computational tool. For this kind of work natural (piperine, curcumin, quercetin) as well as synthetic (Verapamil) bioenhancers were docked against human P-gp (PDB code: 6C0V) and binding en

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Burle, Sushil S., Krishna R. Gupta, Yogeshri J. Jibhkate, Atul T. Hemke, and Milind J. Umekar. "Insights into molecular docking: A comprehensive view." International Journal of Pharmaceutical Chemistry and Analysis 10, no. 3 (2023): 175–84. http://dx.doi.org/10.18231/j.ijpca.2023.030.

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Molecular docking software is mainly used in drug development. Molecular docking offers a wide range of useful techniques for the creation and analysis of pharmaceuticals. Before now, predicting the target for a receptor was extremely challenging however, docking the target protein with a ligand is a straightforward and dependable procedure presently and binding affinity is designed. To see a molecule's three-dimensional structure, a variety of docking tools have been created. The docking score can also be examined using a variety of computational techniques. This review mainly emphases on the

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Vepuri, S. B., S. Anbazhagan, and Rajendra Prasad Y. "Human Aldose Reductase Inhibition By (2E)-1-(5-bromothiophen-2-yl)-3- (2-bromophenyl)prop-2-en-1-one – Structure Based Lead Identification By Induced Fit Docking (IFD) Study of the Ligand Crystal Structure Conformation." International Journal of Drug Design and Discovery 3, no. 4 (2025): 955–63. https://doi.org/10.37285/ijddd.3.4.10.

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Solid state structure information for (2E)-1-(5-bromothiophen-2-yl)-3-(2-bromophenyl)prop-2-en-1-one is revealed by using single crystal x-ray diffraction study. The conformation of the molecule in solid state is used to carry out the drug design studies like structure optimization by Density Functional Theory (DFT) and Induced Fit Docking (IFD) study on human aldose reductase. Docking experiments were conducted for the crystal structure conformation inside AR active site using Maestro 9.1v. from Schrödinger Suite 2009. GLIDE scoring function was used to calculate the dock score. The co-crysta

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Kolageri, Shivanand, Hemanth S, and Mahesh Parit. "In-silico ADME prediction and molecular docking study of novel benzimidazole-1,3,4-oxadiazole derivatives as CYP51 inhibitors for antimicrobial activity." Journal of Applied Pharmaceutical Research 10, no. 3 (2022): 18–27. http://dx.doi.org/10.18231/j.joapr.2022.10.3.28.38.

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A class of innovative benzimidazole-1,3,4-Oxadiazole derivatives is a significant heterocyclic molecule for therapeutic development. In heterocyclic chemistry, the novel 1,3,4-Oxadiazole nucleus has a wide range of uses, including antibacterial, treatment. Molecular docking is frequently employed in contemporary drug design to comprehend drug-receptor interaction. Swiss dock, PyRx, and discovery studio visualizer (DSV) tools were used to predict in-silico ADME properties. In the current investigation, substituted benzimidazole-1,3,4-Oxadiazole derivatives were taken for docking studies against

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Retna, A. Malar, P. Ethalsha, and J. Lydia. "DOCKING SCORE OF THE ISOLATED COMPOUND: 19-HYDROXY LOCHNERICINE - WITH DIFFERENT PROTEINS." Green Chemistry & Technology Letters 2, no. 1 (2016): 31–34. http://dx.doi.org/10.18510/gctl.2015.216.

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It evaluates the inhibitory effect of the isolated compound with different drug targets for the anti-cancer activities. The present investigation analyses the docking score of the isolated compound with different proteins. Two types of proteins (Drug targets) were chosen against cancer namely Human Epidermal Growth Factor and Crystal structure of human placental aromatase cytochrome P450.This result reveals that the compound 19-Hydroxy lochnericine shows hydrogen interactions with the docking energy of – 7.41 and -7.15 –8.83 kcal/mol. This reveals a significant interaction between the target p

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Breda, Ardala, Luiz Basso, Diogenes Santos, and Walter de Azevedo Jr. "Virtual Screening of Drugs: Score Functions, Docking, and Drug Design." Current Computer Aided-Drug Design 4, no. 4 (2008): 265–72. http://dx.doi.org/10.2174/157340908786786047.

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Fukunishi, Yoshifumi, Satoshi Yamasaki, Isao Yasumatsu, Koh Takeuchi, Takashi Kurosawa, and Haruki Nakamura. "Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction." Molecular Informatics 36, no. 1-2 (2016): 1600013. http://dx.doi.org/10.1002/minf.201600013.

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Nguyen, Duc Duy, and Guo-Wei Wei. "AGL-Score: Algebraic Graph Learning Score for Protein–Ligand Binding Scoring, Ranking, Docking, and Screening." Journal of Chemical Information and Modeling 59, no. 7 (2019): 3291–304. http://dx.doi.org/10.1021/acs.jcim.9b00334.

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Shukla, Karuna S., Shailendra Pandey, and A. Pooja Chawla. "SYNTHESIS, BIOLOGICAL EVALUATION AND DOCKING STUDIES OF NON HEPATOTOXIC 5-SUBSTITUTED THIAZOLIDINE-2, 4-DIONES AS ANTIDIABETIC, ANTI-HYPERLIPIDEMIC, ANTI-OXIDANT AND CYTOTOXIC AGENTS." INDIAN DRUGS 57, no. 09 (2020): 19–37. http://dx.doi.org/10.53879/id.57.09.12186.

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A series of eleven thiazolidine-2, 4-dione (TZD) derivatives, were synthesized and characterized by FT-IR, 1 H NMR and mass spectral analysis. All the synthesized TZD derivatives were screened for their in vitro and in vivo anti-diabetic and antioxidant, activities and cytotoxicity. In vivo antihyperglycemic effect was assessed by measuring plasma glucose (PG) levels in alloxan-induced type II diabetic rat models. The compound 4h exhibited better blood glucose lowering activity than the standard drug rosiglitazone. The synthesized TZD derivatives were evaluated for hepatotoxicity and pancreati

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Sahu, Shobharam, Chhaya Rathor Sahu, Divakar Kanakagiri, and Jitender Kumar Malik. "In-Silico Validation of Niazinin-A Against Proinflammatory Mediator: Anti-Proliferative Potential." Saudi Journal of Medical and Pharmaceutical Sciences 9, no. 10 (2023): 720–28. http://dx.doi.org/10.36348/sjmps.2023.v09i10.005.

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Background: Cancer is one of the most dreaded human diseases, that has become an ever-increasing health problem and is a prime cause of death globally. Munga, also known as Moringa oleifera Lam., is one of the most significant plants grown extensively in India. This plant, Moringa oleifera Lam, is used extensively as a dietary supplement and has valuable pharmacological properties including anti-asthmatic, anti-diabetic, hepatoprotective, anti-inflammatory, anti-cancer, antimicrobial, anti-oxidant, cardiovascular, anti-ulcer, CNS activity, anti-allergic, wound healing, analgesic, and antipyret

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Holmes, Samuel G., and Umesh R. Desai. "Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins." Biomolecules 13, no. 11 (2023): 1633. http://dx.doi.org/10.3390/biom13111633.

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Although molecular docking has evolved dramatically over the years, its application to glycosaminoglycans (GAGs) has remained challenging because of their intrinsic flexibility, highly anionic character and rather ill-defined site of binding on proteins. GAGs have been treated as either fully “rigid” or fully “flexible” in molecular docking. We reasoned that an intermediate semi-rigid docking (SRD) protocol may be better for the recapitulation of native heparin/heparan sulfate (Hp/HS) topologies. Herein, we study 18 Hp/HS–protein co-complexes containing chains from disaccharide to decasacchari

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Vidhya Rekha, Umapathy. "Molecular docking analysis of bioactive compounds from Plectranthus amboinicus with glucokinase." Bioinformation 18, no. 3 (2022): 261–64. http://dx.doi.org/10.6026/97320630018261.

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Natural remedies from medicinal plants are known to be effective and reliable appropriate medicine for illnesses. The current research examined Plectranthus amboinicus’ anti diabetic property by docking the bioactive compounds of certain target proteins. We document the molecular docking analysis of bioactive compounds from Plectranthus amboinicus with protein Glucokinase. Molecular docking experiments were carried out in PyRx software. Results of these docking experiments showed that most of the compounds showed very strong interaction with the target protein Glucokinase. Based on the scoring

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Rajendran, Sudha, Nithya G, Brindha Devi P, and Charles C. Kanakam. "DOCKING ANTIOXIDANT ACTIVITY ON HYDROXY (DIPHENYL) ACETICACID AND ITS DERIVATIVES." Asian Journal of Pharmaceutical and Clinical Research 10, no. 7 (2017): 263. http://dx.doi.org/10.22159/ajpcr.2017.v10i7.18299.

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Objectives: The antioxidant activity of the synthesized compounds along with the standard compound for comparison is reported. There is comparison of binding analysis and the ligand interaction of the compound. Methods: The protein crystal structure complexed with 4-methyl-6-[2-(5-morpholin-4-ylpyridin-3-yl)ethyl]pyridin-2-amine inhibitor was selected from Protein Data Bank (5FVP) for our study. Results: The docking studies and structure-activity relationship reveals that the compound 2’-chloro-4-methoxy-3nitro benzilic acid after three different docking strategies reveals that the score was f

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Bano, Shayara, and Jitender K. Malik. "Chlorogenic Acid a Potent Anti-inflammatory Agent: In-Silico Molecular Docking approach." Middle East Research Journal of Pharmaceutical Sciences 2, no. 1 (2021): 10–20. http://dx.doi.org/10.36348/merjps.2022.v02i01.002.

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Abstract: Chlorogenic acid (5-O-caffeoylquinic acid) is a phenolic compound of the hydroxycinnamic acid family. This polyphenol has many health-enhancing properties, most of which are relevant for the treatment of metabolic syndrome, including antioxidant, anti-inflammatory, antilipidemic, antidiabetic, and antihypertensive effects. In addition, chlorogenic acid has antioxidant properties, especially against lipid oxidation. Protective properties against degradation and prebiotic activity of other bioactive compounds present in foods. In addition, chlorogenic acid has antioxidant properties, e

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