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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
Mon Aug 01 2011
Journal Name
Journal Of Engineering
DESIGN OF A CONTINUOUS SLIDING MODE CONTROLLER FOR THE ELECTRONIC THROTTLE VALVE SYSTEM
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Lowering the emission, fuel economy and torque management are the essential
requirements in the recent development in the automobile industry. The main engine control
input that satisfies the above requirements is the throttling angle which adjusts the air mass
flow rate to the engine port. Due to the uncertainty and the presence of the nonlinear
components in its dynamical model, the sliding mode control theory is utilized in this work
for the throttle valve angle control system to design a robust controller for this system in the
presence of a nonlinear spring and Coulomb friction. A continuous sliding mode control law
which consists of a saturation function, instead of a signum function, and the integral of
ano

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Publication Date
Tue Oct 13 2015
Journal Name
Plos Medicine
P2RX7 Purinoceptor: A Therapeutic Target for Ameliorating the Symptoms of Duchenne Muscular Dystrophy
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Publication Date
Fri Nov 01 2024
Journal Name
Egyptian Journal Of Aquatic Biology And Fisheries
Heavy Metals Levels in the Al-Shamiyah River: A Lotic Ecosystem Case Study
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Monitoring lotic ecosystems is vital for addressing sustainability issues. The Al-Shamiyah River is the primary source of water for various daily activities in the Al-Shamiyah district. This study assessed the pollution levels of the river by measuring the concentration and distribution of heavy metals—specifically chromium, cadmium, manganese, copper, zinc, and lead—in both the river's water and sediments. The concentrations of heavy metals in the water ranged from 0.05 to 1.44µg/ L for copper (Cu), 1.57 to 7.25µg/ L for manganese (Mn), 0 to 1.7µg/ L for cadmium (Cd), 0.02 to 1.33µg/ L for lead (Pb), 0.08 to 2.74µg/ L for zinc (Zn), and 0.44 to 1.84µg/ L for chromium (Cr). In the particulate phase, the concentrations ranged from

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Publication Date
Fri Dec 31 2021
Journal Name
Political Sciences Journal
Pakistan: The most dangerous terrorist extremism hotbed (a study information, limitations, and factors)
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   Receipt date:10/27/2021    accepted date:12/15/2021     Publication date:31/12/2021

        Creative Commons License This work is licensed under a Creative Commons Attribution 4.0 International License.

The phenomenon of extremist extremism (terrorism) was one of the most prominent issues that took a large space in the twenty-first century, in which cognitive motives were mixed with strategic and ideological motives, leading to the emergence of terrorist extremi

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Publication Date
Fri Apr 22 2022
Journal Name
Galore International Journal Of Health Sciences And Research
Use of Flavonoids and Green Tea Extracts as Antioxidants Induced by Oxidative Stress: A Review Article
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The aim of this work is to shed light on the importance of medicinal plants, especially those that have extracts that have a direct effect on human health. The study and identification of botany is necessary because human life has become closely linked to the life of plants as food . In addition to using plants as food, primitive man did not stop at this point, but rather developed their use to hunt prey and also used toxic plant materials in wars. With the passage of time, the ancient man was able to link the wild plants that cover the surface of the earth and the diseases that afflict him, so he used these plants or Parts of it are for treatment. A medicinal plant is defined as one or more of its parts that contain one or more che

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Publication Date
Sun Oct 01 2023
Journal Name
Baghdad Science Journal
Green synthesis of CdS:Sn NPs by Starch as a Covering Agent and Studying its Physical Properties
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The aim of this research is to employ starch as a stabilizing and reducing agent in the production of CdS nanoparticles with less environmental risk, easy scaling, stability, economical feasibility, and suitability for large-scale production. Nanoparticles of CdS have been successfully produced by employing starch as a reducing agent in a simple green synthesis technique and then doped with Sn in certain proportions (1%, 2%, 3%, 4%, and 5%).According to the XRD data, the samples were crystallized in a hexagonal pattern, because the average crystal size of pure CdS is 5.6nm and fluctuates in response to the changes in doping concentration 1, 2, 3, 4, 5 %wt Sn, to become   4.8, 3.9, 11.5, 13.1, 9.3 nm respectively. An increase in crystal

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Publication Date
Sun Feb 10 2019
Journal Name
Drug Invention Today
Design, characterization, and in vitro evaluation of zaltoprofen solid dispersion as a hollow-type rectal suppository
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Aim: The present study aims to improve the poor water solubility of zaltoprofen which is a non-steroidal anti-inflammatory drug (NSAIDs) with a potent analgesic effect using solid dispersion then formulate it as a hollow type suppository to be more convenient for geriatric patients. Materials and Method: Zaltoprofen solid dispersions were prepared by solvent evaporation technique in different zaltoprofen: Soluplus® ratios. Results: Among the formulations tested, zaltoprofen solid dispersion preparation using 1:5 (zaltoprofen: Soluplus®) ratio showed the highest solubility and selected for further investigation. Solid dispersion characterization was evaluated by differential scanning calorimetry (DSC), X-ray diffraction study (XRD) and Fou

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Publication Date
Fri Apr 01 2022
Journal Name
Galore International Journal Of Health Sciences And Research
Use of Flavonoids and Green Tea Extracts as Antioxidants Induced by Oxidative Stress: A Review Article
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The aim of this work is to shed light on the importance of medicinal plants, especially those that have extracts that have a direct effect on human health. The study and identification of botany is necessary because human life has become closely linked to the life of plants as food. In addition to using plants as food, primitive man did not stop at this point, but rather developed their use to hunt prey and also used toxic plant materials in wars. With the passage of time, the ancient man was able to link the wild plants that cover the surface of the earth and the diseases that afflict him, so he used these plants or Parts of it are for treatment. A medicinal plant is defined as one or more of its parts that contain one or more chemicals in

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Publication Date
Mon Dec 18 2017
Journal Name
Al-khwarizmi Engineering Journal
Fabrication and Characterization of Tri Metal Oxides by Chemical Spray Pyrolysis Technique as a Gas Sensor
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In this research tri metal oxides were fabricated by simple chemical spray pyrolysis technique from (Sn(NO3)2.20 H2O, Zn(NO3)2.6 H2O, Cd(NO3)2.4 H2O) salts at concentration 0.1M with mixing weight ratio 50:50 were fabricated on silicon substrate n-type (111). (with & without the presence of grooves by the following diemensions (20μm width, 7.5μm depth) with thickness was about ( 0.1 ±0.05 µm) using water soluble as precursors at a substrate temperature 550 ºC±5, with spray distance (15 cm) and their gas sensing properties toward H2S gas at different concentrations (10,50,100,500 ppmv) in air were investigated at room te

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Publication Date
Mon Feb 11 2019
Journal Name
Journal Of Pharmaceutical Sciences And Research
Design of experiments model for optimization of spectrophotometric determination of phenylephrine hydrochloride in pure and pharmaceutical formulations using p-bromanil
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A simple, fast, inexpensive and sensitive method has been proposed to screen and optimize experimental factors that effecting the determination of phenylephrine hydrochloride (PHE.HCl) in pure and pharmaceutical formulations. The method is based on the development of brown-colored charge transfer (CT) complex with p-Bromanil (p-Br) in an alkaline medium (pH=9) with 1.07 min after heating at 80 °C. ‘Design of Experiments’ (DOE) employing ‘Central Composite Face Centered Design’ (CCF) and ‘Response Surface Methodology’ (RSM) were applied as an improvement to traditional ‘One Variable at Time’ (OVAT) approach to evaluate the effects of variations in selected factors (volume of 5×10-3 M p-Br, heating time, and temperature) on

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