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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
Wed Feb 12 2025
Journal Name
Chemchemtech
A REVIEW OF ANALYTICAL METHODS FOR THE ANALYSIS OF PHARMACEUTICALS IN ENVIRONMENTAL SAMPLES
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One of the main causes for concern is the widespread presence of pharmaceuticals in the environment, which may be harmful to living things. They are often referred to as emerging chemical pollutants in water bodies because they are either still unregulated or undergoing regulation. Pharmaceutical pollution of the environment may have detrimental effects on ecosystem viability, human health, and water quality. In this study, the amount of remaining pharmaceutical compounds in environmental waters was determined using a straightforward review. Pharmaceutical production and consumption have increased due to medical advancements, leading to concerns about their environmental impact and potential harm to living things due to their increa

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Publication Date
Fri Feb 28 2020
Journal Name
Neuroquantology
Using X-Ray Films for Evaluation efficiency of Unsaturated Polyester Reinforced by Lead Oxide as Shielding for Medical X-ray Devices
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The largest use of x-ray in medical by dentists, employers or persons that needed by patients with specific conditions, lead to higher exposure of x-ray that may cause many diseases. In the present work radiography films have been used in evaluating the efficiency of using unsaturated polyester polymer reinforced with lead oxide (PbO) as shield material for medical x-ray devices, many parameters studied like concentration and thickness that they are increasing the attenuation of x-ray in them. The results show that the attenuation of X-ray increasing with concentration of reinforced material and with thickness, and the optical density decreases with increasing concentration from 0% to 50%, we chose 30% as suitable concentration to increase

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Publication Date
Tue Jun 17 2025
Journal Name
Baghdad Science Journal
Utilizing an Atomic Force Microscopy with Continuous Flow Injection Analysis using NAG-4(sources)x3 with Three Solar Cells (NAG-4SX3-3D) Analyzer for Studying the Surface Morphology of the Precipitate of the Cyproheptadine-HCl and Loratadine
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Publication Date
Mon Sep 13 2021
Journal Name
Eureka: Physics And Engineering
A numerical study to improve the position and angle of the producer gas injector inside the intake manifold to minimize emissions and efficiency enhancement of a bi engine
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To develop a petrol engine so that it works under the bi-engine pattern (producer gas-petrol) without any additional engine modifications, a single-point injection method inside the intake manifold is a simple and inexpensive method. Still, it leads to poor mixing performance between the air and producer gas. This deficiency can cause unsatisfactory engine performance and high exhaust emissions. In order to improve the mixing inside the intake manifold, nine separate cases were modelled to evaluate the impact of the position and angle orientation inside the intake manifold on the uniformity and spread of the mixture under AFR=2.07. A petrol engine (1.6 L), the maximum engine speed (8000 rpm), and bi-engine mode (petrol-producer ga

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Influence of Organizational Power on the Achievement of Entrepreneurship for Business Organizations An Analytical Study of the Views of a Sample of Managers in the Iraqi Ministry of Education
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This research aims to study the influence of organizational power on the achievement of entrepreneurship for business organizations. It is an analytical study of the views of a sample of managers in the Iraqi Ministry of Education. The research highlights the contribution that can be made from the knowledge of the theory of business organizations in achieving organizational success. The organizational power of the organization contributes to achieving entrepreneurship in the business environment and achieving a competitive position in the work environment. The research dealt with two variables: the first is the independent variable, the organizational power in its dimensions (Expend Power, Structural Power, Prestige Power). And t

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Publication Date
Sat Jul 22 2023
Journal Name
Journal Of Engineering
Experimental Study of a Biomechanical Behaviour of Rat Patellar Tendon
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Tendon is important structure of the human body, since it can sustain tensile loading. The primary function of this tissue is to stabilize the joints they attached to it during daily activities. As well as, tendon has viscoelastic properties that can determine their response to loading and restrict the potential of injuries. One of the major points that this paper works with is the study of the biomechanical behaviour of tendon in response to tensile loading to describe their biological behaviour. Also, conclude the mathematical expression that may illustrate the tendon behaviour. All of the experiments were made in Physiology laboratories / Medical College/ Al- Nahrain University on ten rats "Rattus Norvegicus" of [108- 360] gm weight f

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of The College Of Languages (jcl)
A Stylistic Study of English Aphorisms of “Life and Death”
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In this paper , some of lexical stylistic , syntactical stylistic  devices , and one phonetic stylistic device are going to be illustrated in the study of the aphorisms of “life and death” . These stylistic  devices are parallelism , hyperbole , alliteration , meiosis , irony , oxymoron , cliché , litotes , metalepsis , and loose sentences.  This paper aims at identifying the functions and the  frequencies of these devices. These stylistic devices make one speech and writing more interesting and help to get the attention of readers/ listeners

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Publication Date
Wed Aug 19 2020
Journal Name
Applied Water Science
Spiral path three phase fluidized bed reactor for treating wastewater contaminated with engine oil
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Abstract<p>In this study, a new type of circulating three-phase fluidized bed reactor was conducted by adding a spiral path and was named as spiral three-phase fluidized bed reactor (TPFB-S) to investigate the possibility for removing engine oil (virgin and waste form) from synthetic wastewater by using Ricinus communis (RC) leaves natural and activated by KOH. The biosorption process was conducted by changing particle diameter in the range 150–300 and 300–600 µm, liquid flow rate in the range 2.5–4.5 L/min and gas flow rate in range of 0–1 L/min, while other parameters initial oil emulsion concentration, pH, adsorbent concentration, agitation speed and contact time were kept constant at 2000 mg/L, 2,</p> ... Show More
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Publication Date
Thu May 01 2025
Journal Name
Process Safety And Environmental Protection
Electromembrane extraction of Cadmium (II) using a novel design of electrochemical cell with a flat sheet supported liquid membrane
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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Synthesis, Characterization and study biologicalactivity of several 1-cyclopentene-1,2-dicarboxylimidyl Containing oxadiazole and Benzothiazole
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In this work involved prepared of several new 1-cyclopentene-1,2-dicarboxylimide linked to oxadiazole and benzothiazole moiety were synthesized by two steps: The first step 2-amino-substituted-1,3,4-oxadiazoles and substituted-2-aminobenzothiazole were reaction with 1-cyclopentene-1,2-dicarboxyl anhydride producing N-( 5- substituted-1,3,4-oxadiazole-2-yl)-1-cyclopentene-1,2-dicarboxyl amic acids and N-(Substitutedbenzothiazole-2-yl)-1-cyclopentene-1,2-dicarboxyl amic acids which in turn were dehydrated in the second step via fusion method to afford he desirable N-(5-substituted-1,3,4-oxadiazole-2-yl)-1-cyclopentene-1,2-dicarboxylimides and N-(Substituted benzothiazole-2-yl)1-cyclopentene-1,2-dicarboxylimides respectively. Struct

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