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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 Feb 01 2018
Journal Name
Journal Of Us-china Public Administration
Victims of Terrorism between Compensation and Loss of Rights: A Comparative Study between Iraqi Law and French Law
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The problem of the damage caused by terrorist acts has raised many difficulties in many countries, including Iraq, which requires the existence of a law that sets out sufficient rules for compensating the victims of terrorist acts, in order to compensate them for the harm they have not suffered. It may be difficult or impossible for them to identify causing damage, and therefore unable to obtain compensation by applying the traditional rules of liability that require proof of fault and identify the culprit. The security funds come as an appropriate alternative that pays compensation in such cases for victims to reparation for the damage they suffered. Therefore, this problem remains one of the most problems that Iraq suffers from it, which

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Publication Date
Fri Jul 28 2023
Journal Name
The Journal Of Physical Chemistry A
Tubular Magnetic Shielding Scan (TMSS): A New Technique for Molecular Space Exploration. (i) The Case of Aromaticity of Benzene and [<i>n</i>]Paracyclophanes
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Both traditional and novel techniques were employed in this work for magnetic shielding evaluation to shed new light on the magnetic and aromaticity properties of benzene and 12 [n]paracyclophanes with n = 3–14. Density functional theory (DFT) with the B3LYP functional and all-electron Jorge-ATZP and x2c-TZVPPall-s basis sets was utilized for geometry optimization and magnetic shielding calculations, respectively. Additionally, the 6-311+G(d,p) basis set was incorporated for the purpose of comparing the magnetic shielding results. In addition to traditional evaluations such as NICS/NICSzz-Scan, and 2D-3D σiso(r)/σzz(r) maps, two new techniques were implemented: bendable grids (BGs) and cylindrical grids (CGs) of ghost atoms (Bqs). BGs a

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
A Comparative Study of Some Methods of Estimating Robust Variance Covariance Matrix of the Parameters Estimated by (OLS) in Cross-Sectional Data
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Abstract

The Classical Normal Linear Regression Model Based on Several hypotheses, one of them is Heteroscedasticity as it is known that the wing of least squares method (OLS), under the existence of these two problems make the estimators, lose their desirable properties, in addition the statistical inference becomes unaccepted table. According that we put tow alternative,  the first one is  (Generalized Least Square) Which is denoted by (GLS), and the second alternative is to (Robust covariance matrix estimation) the estimated parameters method(OLS), and that the way (GLS) method neat and certified, if the capabilities (Efficient) and the statistical inference Thread on the basis of an acceptable

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Publication Date
Tue Aug 02 2022
Journal Name
International Journal Of Research In Social Sciences &amp; Humanities
The Making of a Heroine: A Female Character as Portrayed in The English Patient By Michael OndaatjE
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This article discusses how women have significant abilities to cope with the difficulties of war times. They are not the weak and vulnerable victims who are thought to be. On the contrary, they have the power to control over many-sided fronts, like participating in the battlefield as nurses or activists for peace, or even fighters, as well as through the tasks and responsibilities assigned to them to protect and support their families during wartime. The researcher will examine the impact of war upon women. Like men, women suffer during wartime. They are being injured, tortured and killed. Yet, they are able to give examples of love and courage even in the difficult times of war. Hana is one of those women who lived during wartimes,

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Publication Date
Tue Nov 19 2024
Journal Name
Review Of Clinical Pharmacology And Pharmacokinetics - International Edition
Clinical use of tumor necrosis factor-alpha inhibitors in Iraq: a review of their documented efficacy, safety, and associated genetics
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This comprehensive review examines the efficacy and safety of tumor necrosis factor-alpha (TNF-α) inhibitors in treating various autoimmune diseases, and focuses on their application in Iraqi patients. Elevated TNF-α levels are linked to autoimmune disorders, leading to the development of anti-TNF-α therapies such as infliximab, etanercept, adalimumab, certolizumab pegol, and golimumab, which have gained FDA approval for conditions like psoriasis, in¬flammatory bowel disease, ankylosing spondylitis, and rheumatoid arthritis. While these therapies demonstrate sig¬nificant therapeutic benefits, including improved quality of life and disease management, they also carry risks, such as increased susceptibility to infections and pote

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Publication Date
Tue Apr 01 2025
Journal Name
Journal Of Economics And Administrative Sciences
Spatial Quantile Autoregressive Model: A Review
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This paper is specifically a detailed review of the Spatial Quantile Autoregressive (SARQR) model that refers to the incorporation of quantile regression models into spatial autoregressive models to facilitate an improved analysis of the characteristics of spatially dependent data. The relevance of SARQR is emphasized in most applications, including but not limited to the fields that might need the study of spatial variation and dependencies. In particular, it looks at literature dated from 1971 and 2024 and shows the extent to which SARQR had already been applied previously in other disciplines such as economics, real estate, environmental science, and epidemiology. Accordingly, evidence indicates SARQR has numerous benefits compar

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Publication Date
Tue Feb 28 2023
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Bitcoin Prediction with a hybrid model
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. In recent years, Bitcoin has become the most widely used blockchain platform in business and finance. The goal of this work is to find a viable prediction model that incorporates and perhaps improves on a combination of available models. Among the techniques utilized in this paper are exponential smoothing, ARIMA, artificial neural networks (ANNs) models, and prediction combination models. The study's most obvious discovery is that artificial intelligence models improve the results of compound prediction models. The second key discovery was that a strong combination forecasting model that responds to the multiple fluctuations that occur in the bitcoin time series and Error improvement should be used. Based on the results, the prediction a

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Publication Date
Wed Feb 01 2023
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Bitcoin Prediction with a hybrid model
...Show More Authors

In recent years, Bitcoin has become the most widely used blockchain platform in business and finance. The goal of this work is to find a viable prediction model that incorporates and perhaps improves on a combination of available models. Among the techniques utilized in this paper are exponential smoothing, ARIMA, artificial neural networks (ANNs) models, and prediction combination models. The study's most obvious discovery is that artificial intelligence models improve the results of compound prediction models. The second key discovery was that a strong combination forecasting model that responds to the multiple fluctuations that occur in the bitcoin time series and Error improvement should be used. Based on the results, the prediction acc

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Scopus (10)
Scopus
Publication Date
Tue Apr 01 2025
Journal Name
Journal Of Economics And Administrative Sciences
Spatial Quantile Autoregressive Model: A Review
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This paper is specifically a detailed review of the Spatial Quantile Autoregressive (SARQR) model that refers to the incorporation of quantile regression models into spatial autoregressive models to facilitate an improved analysis of the characteristics of spatially dependent data. The relevance of SARQR is emphasized in most applications, including but not limited to the fields that might need the study of spatial variation and dependencies. In particular, it looks at literature dated from 1971 and 2024 and shows the extent to which SARQR had already been applied previously in other disciplines such as economics, real estate, environmental science, and epidemiology. Accordingly, evidence indicates SARQR has numerous benefits compar

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Publication Date
Tue Apr 25 2023
Journal Name
Journal Of Periodontal Research
Salivary E‐cadherin as a biomarker for diagnosis and predicting grade of periodontitis
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Abstract<sec><title>Objectives

To determine the abilities of salivary E‐cadherin to differentiate between periodontal health and periodontitis and to discriminate grades of periodontitis.

Background

E‐cadherin is the main protein responsible for maintaining the integrity of epithelial‐barrier function. Disintegration of this protein is one of the events associated with the destructive forms of periodontal disease leading to increase concentration of E‐cadherin in the oral biofluids.

Materials and Methods

A total of 63 patients with periodontitis (case) and 35

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