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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Thu Mar 25 2021
Journal Name
Dental Materials Journal
Mechanical and thermal stress evaluation of PEEK prefabricated post with different head design in endodontically treated tooth: 3D-finite element analysis
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Publication Date
Mon Aug 05 2024
Journal Name
Food And Bioprocess Technology
Development of an Innovative Reinforced Food Packaging Film Based on Corn Starch/Hydroxypropyl Methylcellulose/Nanocrystalline Cellulose Incorporated with Nanogel Containing Quercetin
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Publication Date
Wed Apr 01 2020
Journal Name
Biochemical And Cellular Archives
Immunohistochemical evaluation of epidermal growth factor expression in skin wound treated by capparis spinosa flavonoid extract in alloxan induced diabetes rats
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In diabetes, impaired wound healing and other tissue abnormalities are considered major concerns. Many factorsaffect the time and quality of wound healing. One of the purposes of medical sciences is wound healing in a short time withreduced side effects. The herbal products are more precious in both prophylaxis as well as curative in delayed diabetic woundhealing activity when compared to synthetic drugs.A wide range of evidence has shown that capers plant possesses differentbiological effects, including antioxidant, anticancer and antibacterial effects. Phytochemical analysis shows thatC. spinosahashigh quantities of bioactive constituents, including polyphenolic compounds, which are responsible for its health-promotingeffects. The healing

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Publication Date
Sat Oct 29 2022
Journal Name
International Ophthalmology
Comparison of corneal flap thickness predictability and architecture between femtosecond laser and sub-Bowman keratomileusis microkeratome in laser in situ keratomileusis
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Publication Date
Sun Mar 01 2020
Journal Name
Baghdad Science Journal
Evaluation of Sex Hormone Levels in Benign Prostatic Hyperplasia Patients Treated with 5 Alpha-Reductase Inhibitor (Finasteride) in Amara city/Iraq
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The present study aimed to determine the serum sex hormone levels among Benign Prostatic Hyperplasia (BPH) patients before and after 3 months of oral administration of 5-α reductase inhibitor(finasteride). Forty BPH patients and 40 healthy men from Amara city were involved in this study, their ages were between 40-59 year. They were all subjected  to direct estimation of hormones by MinVidas method including Testosterone (T), Estradiol (E2), Follicle Stimulating Hormone (FSH), Luteinizing Hormone (LH), Prolactin (PRL), and Dihydrotestosterone (DHT) before and after 3 months of treatment with 5α-reductase inhibitor (finasteride) (the healthy individuals didn’t take finasteride).The results showed that T level was significantly lo

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Publication Date
Thu Jan 01 2026
Journal Name
Aip Conference Proceedings
Effects of an augmented motor reality–based training program on spatial awareness and skill-based decision making in youth basketball players
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ew sports technologies have highlighted the importance of perceptual – cognitive training in order to optimize performance in sports e.g., dynamic team sport such as basketball. Augmented motor reality AMR is a new training model based on realistic movement combined with interactive virtual cues that may be useful to enhance spatial orientation and decision making. The purpose of this study was to investigate the effects of an AMR-based training program on spatial awareness and skill-based decision making in youth basketball players. Twenty-four male young basketball players aged 15.2±0.8 years were randomized to the experimental group n=12, receiving AMR training, and control group n=12, performing conventional practice. The interventio

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Publication Date
Tue Jul 18 2023
Journal Name
Research On Chemical Intermediates
Effectual and rapid synthesis of bis(pyrazolyl)methanes and pyrazolopyranopyrimidines catalyzed by nano-[TSPSED][Cl]2 and investigating their biological activity
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This investigation reports application of a mesoporous nanomaterial based on dicationic ionic liquid bonded to amorphous silica, namely nano-N,N,N′,N′-tetramethyl-N-(silican-propyl)-N′-sulfo-ethane-1,2-diaminium chloride (nano-[TSPSED][Cl]2), as an extremely effectual and recoverable catalyst for the generation of bis(pyrazolyl)methanes and pyrazolopyranopyrimidines in solvent-free conditions. In both synthetic protocols, the performance of this catalyst was very useful and general and presented attractive features including short reaction times with high yields, reasonable turnover frequency and turnover number values, easy workup, high performance under mild conditions, recoverability and reusability in 5 consecutive runs without lo

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Publication Date
Tue Aug 22 2023
Journal Name
Advances In Structural Engineering
Experimental and finite element analysis of reinforced concrete multi-cell box girders retrofitted with carbon fiber reinforced polymer strips under torsion
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This study expands the state of the art in studies that assess torsional retrofit of reinforced concrete (RC) multi-cell box girders with carbon fiber reinforced polymer (CFRP) strips. The torsional behavior of non-damaged and pre-damaged RC multi-cell box girder specimens externally retrofitted by CFRP strips was investigated through a series of laboratory experiments. It was found that retrofitting the pre-damaged specimens with CFRP strips increased the ultimate torsional capacity by more than 50% as compared to the un-damaged specimens subjected to equivalent retrofitting. This indicated that the retrofit has been less effective for the girder specimen that did not develop distortion beforehand as a result of pre-loading. From

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Publication Date
Mon Sep 11 2023
Journal Name
Journal Of Chemical Technology & Biotechnology
Modeling and optimization of biodiesel from high free‐fatty‐acid chicken fat by non‐catalytic esterification and mussel‐shell‐catalyzed transesterification
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Abstract<sec><title>BACKGROUND

In this study, biodiesel was prepared from chicken fat via a transesterification reaction using Mussel shells as a catalyst. Pretreatment of chicken fat was carried out using non‐catalytic esterification to reduce the free fatty acid content from 36.28 to 0.96 mg KOH/g oil using an ethanol/ fat mole ratio equal to 115:1. In the transesterification reaction, the studied variables were methanol: oil mole ratio in the range of (6:1 ‐ 30:1), catalyst loading in the range of (9‐15) wt%, reaction temperature (55‐75 °C), and reaction time (1‐7) h. The heterogeneous alkaline catalyst was greenly synthesized from waste mussel shells throughout a calcin

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Publication Date
Fri Nov 11 2011
Journal Name
Journal Of The European Optical Society: Rapid Publications
Transition from amplified spontaneous emission to laser action in disordered media of R6G dye and TiO2 nanoparticles doped with PMMA polymer
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