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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 Jan 30 2014
Journal Name
Al-kindy College Medical Journal
Effects of Sleeve Gastrectomy as a Bariatric Surgery on Weight of Dietary Induced Obese Rats.
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Background: Obesity is becoming the healthcare epidemic world wide.Obesity is associated with reduced life expectancy, increased morbidity and mortality, and greater healthcare costs.Bariatric surgery is the only effective treatment for morbid obesity and is gaining increasing popularity. There has been a steady rise in the numbers and types of bariatric operations done worldwide in recent years butnon of prove to be ideal .Animal studies and use of animal models are significant element in the evolution of medical knowledge and the use of animals as a model for bariatric surgery is of importance to study the mechanisms of these operationsa and also help to develop new technique in management of obesity.Objectives:Study of effects of slee

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Publication Date
Mon Jan 01 2024
Journal Name
Computer Modeling In Engineering & Sciences
A Review and Bibliometric Analysis of the Current Studies for the 6G Networks
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Publication Date
Sun Mar 13 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Isolation and Identification of food Probiotic Saccharomyces boulardii by using traditional methods, Vitek 2 system and molecular identification methods.: Isolation and Identification of food Probiotic Saccharomyces boulardii by using traditional methods, Vitek 2 system and molecular identification methods.
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This study was aimed to isolate and identify Saccharomyces boulardii from Mangosteen fruits (Garcinia mangostana L.) by traditional and molecular identification methods To get safe and healthy foods probiotics for use, The isolates and two commercial strains were subjected to cultural, morphological and biochemical tests, The colonies of the isolates were spherical, smooth, mucoidal, dull and white to cream colour on SD agar media .The shape of cells was globose to ovoid and sometimes with budding, in a single form or clustered like a beehive. The isolates and two commercial strains were unable to metabolized galactose and lactose , Results shows that all isolates were unable to utilize potassium nitrate and not grow in the presence of (

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Publication Date
Mon Nov 01 2021
Journal Name
Proceedings Of First International Conference On Mathematical Modeling And Computational Science: Icmmcs 2020
Study the Stability for Ordinary Differential Equations Using New Techniques via Numerical Methods
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Nonlinear differential equation stability is a very important feature of applied mathematics, as it has a wide variety of applications in both practical and physical life problems. The major object of the manuscript is to discuss and apply several techniques using modify the Krasovskii's method and the modify variable gradient method which are used to check the stability for some kinds of linear or nonlinear differential equations. Lyapunov function is constructed using the variable gradient method and Krasovskii’s method to estimate the stability of nonlinear systems. If the function of Lyapunov is positive, it implies that the nonlinear system is asymptotically stable. For the nonlinear systems, stability is still difficult even though

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Determinants of Investment Allocations in the Agricultural Sector in Iraq : A Comparison Between the Method of least Squares Approach and the errror Correction Model
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Abstract

                 The research aimed to test the relationship between the size of investment allocations in the agricultural sector in Iraq and their determinants using the Ordinary Least Squares (OLS) method compared to the Error Correction Model (ECM) approach. The time series data for the period from 1990 to 2021 was utilized. The analysis showed that the estimates obtained using the ECM were more accurate and significant than those obtained using the OLS method. Johansen's test indicated the presence of a long-term equilibrium relationship between the size of investment allocations and their determinants. The results of th

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Publication Date
Wed Apr 01 2015
Journal Name
Journal Of Environmental Engineering
Using Granular Dead Anaerobic Sludge as Permeable Reactive Barrier for Remediation of Groundwater Contaminated with Phenol
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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Simultaneous influences of hematocrit in the erythrocyte medium on erythrocyte aggregation and sedimentation: a kinetic study by a laser scattering technique
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The erythrocyte aggregation is an important physiological phenomenon in the circulation of blood. It is a basic characteristic of normal blood that plays a major role in the cardiovascular system, especially in the microcirculation. This study explained the kinetics of single cells rouleaux formation one- dimensional aggregate and three- dimensional aggregate, during simultaneous, and the effect of hematocrit on the process of aggregation and sedimentation. The present study was done on forty one healthy subjects. Laser light is passed through a well mixed sample of blood and the forward scattered light intensities recorded continuously. The samples were prepared with different hematocrit, (10%, 15%, 20%, and 25%). Increasing

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Publication Date
Mon Jul 03 2023
Journal Name
College Of Islamic Sciences
A critical methodological study in abrogative,abrogated, in a book of (Zad AlTafseer) in Surah Al-Baqara in the holy Quraan.
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This research is a critical methodological  study deals with some Quranic verses abrogative,abrogated.

by Ibn al-Jawzi (may Allah have mercy on him) in his book (Tafseer Zad al-Maseer) inin Surah Al-Baqara the  in the holy Quraan.

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Publication Date
Wed Aug 26 2020
Journal Name
Iraqi Journal Of Agricultural Sciences
COMPARISON THE ACCURACY OF COMPUTING POINT COORDINATS BETWEEN DIFFERENT INSTRUMENTS AND APPLICATIONS OF GPS
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The study was aimed to determine the coordinates of  the points were measured by different ways and different instruments, the most precise way using the differential global positioning system (DGPS) that will be the reference measurements in comparison, less precise way using navigator GPS. Google earth (pro.), and the other applications of GPS mobile ( Samsung and I-phone). In this research (8 points) were chosen that are occasional in location. The comparison of the different observations can give us an idea of ​​the extent to which the accuracy of the observations differs from the different devices used in the observing, as well as through the knowledge of the best device and the best way to measure coordinates accurately t

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Publication Date
Fri Jan 30 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of canal dryness and flaring on the accuracy of two electronic apex locators
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Background: This in vitro study evaluated the effect of canal dryness and flaring on the accuracy of two electronic apex locators for working length (WL) determination. Materials and methods: Sixty extracted teeth were used, after access opening was done, the occlusal surface was flattened to create stable reference point. The teeth were randomly divided into two equal main groups of flared and unflared group each one of 30 teeth. The flaring was done with Gates Glidden drills. The two main groups were further subdivided into two subgroups: dry canal and wet canal using 5.25% sodium hypochlorite groups, Electronic WL of each sample was determined using both Root ZX and i-Root apex locator. Consequently, histologic WL was determined by shav

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