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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 Aug 05 2021
Journal Name
International Journal Of Renewable Energy Development
Desalination of Agricultural Wastewater by Solar Adsorption System: A Numerical Study
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There are still areas around the world suffer from severe shortage of freshwater supplies. Desalination technologies are not widely used due to their high energy usage, cost, and environmental damaging effects. In this study, a mathematical model of single-bed adsorption desalination system using silica gel-water as working pair is developed and validated via earlier experiments. A very good match between the model predictions and the experimental results is recorded. The objective is to reveal the factors affecting the productivity of fresh water and cooling effect in the solar adsorption system. The proposed model is setup for solving within the commercially-available software (Engineering Equation Solver). It is implemented to so

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Publication Date
Mon Sep 04 2017
Journal Name
Journal Of College Of Education For Women
Tagmemic Analysis of English and Arabic Praise Poetry: A Contrastive Study
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This research provides a new method to study praise poetry that can be used as a course to teach English and Arabic to students in the College of Education. This research answers two questions: Is it possible to examine praise poetry as a tagmeme? Is this analysis of great help in teaching English and Arabic to students in the College of Education? The data that will be chosen for the purpose of analysis are two of Shakespeare's sonnets and two of AL Mulik's poems. The sonnets selected for this purpose are 17 and 18. AL Mulik's poems selected for the same purpose are 8 and 9. Each line in both English and Arabic data is numbered by the researcher herself. Then, those lines are grouped into sentences to facilitat

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Publication Date
Thu Feb 07 2013
Journal Name
Iraqi Journal Of Medical Science
A study of serum magnesium and calcium levels in missed abortion
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Publication Date
Fri Dec 29 2017
Journal Name
Al-khwarizmi Engineering Journal
A Study Of Strengthening Circular Diaphragm By Ring-Shaped Concentric Ribs
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 This paper deals with the determination of stresses and deflections of clamped circular diaphragm strengthened by one or two ring-shaped concentric ribs, under uniform static and dynamic pressures. The simulation has been achieved by using the well-known engineering software finite element package MSC/NASTRAN

 As a design study, the effect of using a clamped ring, and the effect of using a ring-shaped rib on both surfaces of diaphragm instead of one, has been discussed in this work. To show the effectiveness of this study, results of this work have been compared with  published data [1].

In  the  conclusion,  the  authors underline  the  validity of  the&n

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Publication Date
Wed Jan 19 2022
Journal Name
Asian Journal Of Water, Environment And Pollution
Air Pollution: A Study of Its Concept, Causes, Sources and Effects
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Air pollution is very important topic for those interested in studying the environment because of its importance and the damage caused by it to human, animal and plant life. This research addresses the concept of air pollution, its causes, and its danger, and sheds light on the influence of climate elements on environmental pollution and the effect of temperature, rain, humidity, wind direction and speed, and atmospheric pressure on the increase or decrease of air pollution. This research discusses the sources of air pollution, including natural ones, including dust, smoke resulting from fires, erupting volcanoes, and others, including those resulting from human uses such as the use of fuel and others. The research addressed the dam

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Publication Date
Mon Dec 30 2013
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Mass Transfer Enhancement Using Extensions as Turbulence Promoters
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Mass transfer was studied using a rotating cylinder electrode with different lengths of legs acting as turbulence promoters. Two types of rotating cylinder ,made of brass, were examined : an enhanced cylinder one, with four rectangular extensions 10 mm long, 10 mm wide, and 1mm thick, and an enhanced cylinder two with four longitudes 30 mm long,10 mm wide, and 1mm thick. The best performance was obtained for enhanced cylinder two at low rotation speeds while enhanced cylinder one was realized at high rotation speeds. The mass transfer enhancement as compared with a normal rotating cylinder electrode, devoid of promoters, is 53% or 58% higher. The enhancement percentage decreased as rotation speeds increased further, since, seemingly, ful

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Publication Date
Wed Dec 10 2025
Journal Name
Cell Biochemistry And Biophysics
Green Tea–Driven Green Synthesis of a Curcumin@Platinum Nanohybrid with Multifunctional Antioxidant, Burn-Healing Agent, and Selective Anticancer against PANC-1 Pancreatic Cancer Cells
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This study aimed to fabricate a curcumin@platinum nanohybrid (CUR@Pt NPs) through a green tea–based synthesis method and to evaluate its various functions, including antioxidant, burn-healing, and selective anticancer activities against PANC-1 pancreatic cancer cells. Green tea polyphenols served as natural reducing and stabilizing agents, facilitating an eco-friendly, single-step manufacturing process. Physicochemical characterization confirmed successful nanohybrid formation: a CUR@Pt band appeared at 457 nm in the UV–Vis spectrum, XRD displayed crystalline platinum peaks at 2θ = 46.9°, and 67.0°, matching the (200), and (220) planes, respectively, and TEM images showed well-dispersed spherical nanoparticles with an average siz

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Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The effect of the marketing channel of the service on marine insurance losses: a case study in the Iraqi insurance company
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All businesses seek to improve their levels of profits through various means, most notably their marketing channels, which ensure the delivery of their products to their customers in a safe manner in a timely manner. It considers losses to a minimum and that insurance companies place great interest in marine insurance losses because they often constitute huge amounts compared to other losses, hence the problem of research, which is centred on the type and size of the impact owned by the channel The Iraqi insurance company was chosen to be applied according to the intentional sample method because this company is closely related to the subject matter. The research has reached a set of conclusions, most notably that the choice of i

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Publication Date
Mon Nov 02 2020
Journal Name
International Journal Of Pharmaceutical Research
Evaluation of Serum Adropin Levels in Nonalcoholic Fatty Liver Disease as A Complication of Hypothyroidism In Iraqi Patients
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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Craniofacial Surgery
Novel Application of Platelet-Rich Fibrin as a Wound Healing Enhancement in Extraction Sockets of Patients Who Smoke
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