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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
Sat Dec 31 2022
Journal Name
Al-kindy College Medical Journal
Assessment of Serum Level of Protein Carbonyl as a Marker of Protein Oxidation in Patients with Type 2 Diabetes Mellitus
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Background: Diabetes mellitus is a chronic disease with an increasing prevalence worldwide and characterized by an increase in oxidative stress and inflammation. The most important factor that is responsible for oxidative stress and production of reactive oxygen species (ROS) is hyperglycemia. The major targets of ROS are proteins. The most common and widely used biomarker of severe oxidative protein damage is protein carbonyl content.

The study was designed to assess the serum level of protein carbonyl as a marker of protein oxidation in patients with type 2 diabetes mellitus and to evaluate the effect of age, body weight, waist circumference, diabetic control and disease duration on the level

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Publication Date
Wed Mar 01 2023
Journal Name
Journal Of Engineering
Comparative Evaluation of Roundabout Capacities Methods for Single-lane and Multi-lane Roundabout
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A roundabout is a highway engineering concept meant to calm traffic, increase safety, reduce stop-and-go travel, reduce accidents and congestion, and decrease traffic delays. It is circular and facilitates one-way traffic flow around a central point. The first part of this study evaluated the principles and methods used to compare the capacity methods of roundabouts with different traffic conditions and geometric configurations. These methods include gap acceptance, empirical, and simulation software methods. Previous studies mentioned in this research used various methods and other new models developed by several researchers. However, this paper's main aim is to compare different roundabout capacity models for acceptabl

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Publication Date
Mon Jan 01 2024
Journal Name
The International Journal Of Central Banking
USING SOME NONPARAMETRIC ESTIMATORS OF THE ERROR CORRECTION MODEL TO MEASURE THE EFFECT OF CHANGES IN BANK DEPOSITS ON THE MONEY SUPPLY
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In this paper, the effect of changes in bank deposits on the money supply in Iraq was studied by estimating the error correction model (ECM) for monthly time series data for the period (2010-2015) . The Philips Perron was used to test the stationarity and also we used Engle and Granger to test the cointegration . we used cubic spline and local polynomial estimator to estimate regression function .The result show that local polynomial was better than cubic spline with the first level of cointegration.

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Publication Date
Sat Nov 12 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The relationship of salary localization and the growth of bank deposits: (applied research for a sample of private banks)
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The research problem consisted in answering the question that revolves around whether there is a relationship to the settlement of salaries with the growth of bank deposits? The research also aimed to provide some initial solutions to improve the role of salary localization, in terms of reviewing the concept of electronic payment systems, its tools and channels, and then identifying the concept of salary localization, its importance, objectives and obstacles to its application, and then analyzing the reality of the state of the settlement of salaries and bank deposits for the research sample banks, which are each of the bank (Ashur International, Business Bay, the Iraqi Middle East for Investment, the Iraqi National, Development and the

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Publication Date
Thu Dec 30 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Design a system for an approved video copyright over cloud based on biometric iris and random walk generator using watermark technique
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Publication Date
Mon Feb 15 2021
Journal Name
Drug Delivery And Translational Research
Breast intraductal nanoformulations for treating ductal carcinoma in situ II: Dose de-escalation using a slow releasing/slow bioconverting prodrug strategy
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Publication Date
Sun Nov 23 2025
Journal Name
Journal Of Administration And Economics
Using the Maximum Likelihood Method with a Suggested Weight to Estimate the Effect of Some Pollutants on the Tigris River- City of Kut
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The aim of this research is to use robust technique by trimming, as the analysis of maximum likelihood (ML) often fails in the case of outliers in the studied phenomenon. Where the (MLE) will lose its advantages because of the bad influence caused by the Outliers. In order to address this problem, new statistical methods have been developed so as not to be affected by the outliers. These methods have robustness or resistance. Therefore, maximum trimmed likelihood: (MTL) is a good alternative to achieve more results. Acceptability and analogies, but weights can be used to increase the efficiency of the resulting capacities and to increase the strength of the estimate using the maximum weighted trimmed likelihood (MWTL). In order to perform t

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Publication Date
Tue Nov 09 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Strategic leadership and its role in achieving competitiveness in industrial establishments": "A field study in Bashir Al-Siksik & Co. for the manufacture of sanitary and plastic tools
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This study aims to know the role of strategic leadership to achieving competitiveness in industrial establishments by identifying the respondents’ perceptions about the level of availability of dimensions of leadership strategies (creativity and innovation, risk tolerance, available opportunities) in Bashir Al-Siksek & Partners Company for the manufacture of sanitary and plastic ware in Gaza strip

To achieve this, a questionnaire was developed and distributed to a sample of managers, auditors, accountants, and administrative employees in the study sample company. The questionnaire tool was distributed to 60 employees and employees, of which (52) were retrieved, or 86.6%, and (8) were excluded for la

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Publication Date
Fri Dec 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
Effect of Addition Different Levels of Kojic Acid and Sodium Alginate as a substitutes of conventional Antibiotic on the Characteristics of Cryopreserved Semen of Buffalo Bulls
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Abstract<p>This experiment examined the effects of adding sodium alginate and KOJIC acid as substitutes of Conventional antibiotics to soybean lecithin extender on the characteristics of cryopreserved and frozen buffalo bull semen, as well as evaluation of their additions as antibiotics that to help lowering the microbial load. Following the collection and dilution of in the soybean lecithin extender, the experimental treatments were separated into five groups, as follows: T1: (control-) without adding any antibiotics; T2: (control+) adding the conventional antibiotics Gentamicin 0.4 IU and Tylosin 0.08 IU per 100 ml; T3: adding Kojic acid at (0.06 g/L) T4: adding sodium alginate at (0.6 mg/mL)T</p> ... Show More
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Publication Date
Tue Aug 02 2016
Journal Name
European Academic Research
‘Resymbolization’ of a Text; a Relatively Different Perspective of Graham Greene’s The Quiet American
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The Quiet American could be considered as one of Graham Greene’s most distinguished books; it is an epochal novel written during the phase of the cold war between the United States and the Soviet Union. The novel deals with the interference of the United States in Vietnam ten years before Vietnam’s war. The role the Americans played in arousing an inner political crisis in the country previous to her military invention. The book reflects that this action was not out of American government concern about Vietnamese people themselves but merely a political foreign affair. They wanted to stop communism from spreading widely and reducing its role in the East. This paper attempts to analyse the novel concentrating on the message Greene intend

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