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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
Mon Jan 13 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Analyzing the net profitability of total investments using a constructed mathematical model: An applied research at Iraqi Middle East Bank for investment for the financial years 2008-2010
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The trading banks in Iraq invest their funds according to regulations imposed by the Central Bank in Iraq in different financial fields like stock exchanges, acquire stocks as assets that could be sold at any time as well as make loans and contributing in corporations establishment also magnitude foreign capital through direct contacts with foreign exchange markets.

We can summarize the problem of this paper as shortage in mathematical models that used in studying and analyzing these investments and according to this problem we used (a constructed mathematical model ) consists of three major indicators: profitability of total investment assets which is divided into three sub-indicators: owners equity risk indicator, debits risk i

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Publication Date
Thu Feb 01 2024
Journal Name
Heliyon
Removal of amoxicillin from contaminated water using modified bentonite as a reactive material
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This study concerns the removal of a trihydrate antibiotic (Amoxicillin) from synthetically contaminated water by adsorption on modified bentonite. The bentonite was modified using hexadecyl trimethyl ammonium bromide (HTAB), which turned it from a hydrophilic to a hydrophobic material. The effects of different parameters were studied in batch experiments. These parameters were contact time, solution pH, agitation speed, initial concentration (C0) of the contaminant, and adsorbent dosage. Maximum removal of amoxicillin (93 %) was achieved at contact time = 240 min, pH = 10, agitation speed = 200 rpm, initial concentration = 30 ppm, and adsorbent dosage = 3 g bentonite per 1L of pollutant solution. The characterization of the adsorbent, modi

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Publication Date
Wed Aug 31 2022
Journal Name
Al-kindy College Medical Journal
A Comparative Study between Transcutaneous Bilirubinometry and Total Serum Bilirubin Measurement in Jaundiced Newborns
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Background: Drawing blood to measure total serum bilirubin is painful & time consuming. Transcutaneous bilirubinometer working by multiwavelength spectral reflectance from the skin surface on forehead or upper sternum is a quick & painless technique. 

Objectives: to compare the effectiveness of transcutaneous (over the upper sternum and forehead) and serum bilirubin measurement of neonate with jaundice.

Subjects and Methods: This is a cross sectional prospective study. It enrolled 175 jaundiced neonates & excluded those exposed to phototherapy. It was conducted at Child Central Teaching Hospi

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Publication Date
Thu Jan 30 2020
Journal Name
Al-kindy College Medical Journal
Chronic Tennis Elbow Treated by Platelet-Rich Plasma Versus Steroid Injections: A Comparative Study
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Background: Painful elbow joint over the lateral epicondyle especially with resisted wrist extension are common signs of lateral epicondyle tendinopathy, also called tennis elbow.

Objective: To evaluate the clinical outcome of local platelet rich plasma (PRP) injection in patients with chronic tennis elbow compared with a steroid (Depomedrol 40 mg) injection.

Methods: A total of 88 patients with chronic tennis elbow were treated at Al-Kindy Teaching Hospital and private clinics. All patients had chronic pain for about 24 weeks or more and had failed first line treatment. The patients dividing into two groups, Group A injected with PRP (n = 44), and group B injected with d

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Publication Date
Thu Jan 30 2020
Journal Name
Al-kindy College Medical Journal
Chronic Tennis Elbow Treated by Platelet-Rich Plasma Versus Steroid Injections: A Comparative Study
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Background: Painful elbow joint over the lateral epicondyle especially with resisted wrist extension are common signs of lateral epicondyle tendinopathy, also called tennis elbow. Objective: To evaluate the clinical outcome of local platelet rich plasma (PRP) injection in patients with chronic tennis elbow compared with a steroid (Depomedrol 40 mg) injection. Methods: A total of 88 patients with chronic tennis elbow were treated at Al-Kindy Teaching Hospital and private clinics. All patients had chronic pain for about 24 weeks or more and had failed first line treatment. The patients dividing into two groups, Group A injected with PRP (n = 44), and group B injected with depomedrol 40 mg (n = 44). A good clinical result w

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Publication Date
Sun Jan 24 2016
Journal Name
Al-academy
Babylonian theater (Its history, models and properties) a historical comparative study: محمد صبري صالح
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The building of the Babylonian theater is considered as one of the distinctive buildings where its foundations have remained steadfast in the face of geographical changes, social's erosion and groundwater that threatened almost all traces of Babylon despite the destruction of the outer structure of the building. The general directorate of antiques performed prospection for those foundations (the ground map), and then the building was completed by new bricks over the original scheme. It became clear when examining the building; its components and foundations, that the building is unique in comparison with the old buildings of the world throughout Iraq. There are similar buildings in other places like Jordan and North Africa such as

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Publication Date
Tue Jan 30 2024
Journal Name
International Journal Of Pharmacy Practice
A Comprehensive Review of Drivers influencing Flu Vaccine Acceptance in the Middle East: Using Health Belief Model
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Rationale, aims and objectives: A review of studies published over the last six years gives update about this hot topic. In the middle of COVID-19 pandemic, this study findings can help understand how population may perceive vaccinations. The objectives of this study were to review the literature covering the perceptions about influenza vaccines and to determine factors influencing the acceptance of vaccination using Health Belief Model (HBM). Methods: A comprehensive literature search was performed utilizing PubMed and Google Scholar databases. Three keywords were used: Influenza vaccine, perceptions, and Middle East. Empirical studies that dealt with people/ HCW perceptions of influenza vaccine in the Middle East and writt

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Publication Date
Mon Feb 21 2022
Journal Name
Applied Sciences
The Behavior of Hybrid Fiber-Reinforced Concrete Elements: A New Stress-Strain Model Using an Evolutionary Approach
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Several stress-strain models were used to predict the strengths of steel fiber reinforced concrete, which are distinctive of the material. However, insufficient research has been done on the influence of hybrid fiber combinations (comprising two or more distinct fibers) on the characteristics of concrete. For this reason, the researchers conducted an experimental program to determine the stress-strain relationship of 30 concrete samples reinforced with two distinct fibers (a hybrid of polyvinyl alcohol and steel fibers), with compressive strengths ranging from 40 to 120 MPa. A total of 80% of the experimental results were used to develop a new empirical stress-strain model, which was accomplished through the application of the parti

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Publication Date
Tue Sep 01 2020
Journal Name
Journal Of Engineering
Optimization and Modeling the Performance of a Mediator-less Microbial Fuel Cell using Butler-Volmer-Monod Model
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In this study, a one-dimensional model represented by Butler-Volmer-Monod (BVM) model was proposed to compute the anode overpotential and current density in a mediator-less MFC system. The system was fueled with various organic loadings of real field petroleum refinery oily sludge to optimize the favorable organic loading for biomass to operate the suggested system. The increase in each organic loading showed higher resistance to electrons transport to the anode represented by ohmic loss. On the contrary, both activation and mass transfer losses exhibited a noticeable decrement upon the increased organic loadings. However, current density was improved throughout all increased loads achieving a maximum current density of 5.2 A/m3

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Publication Date
Thu Jun 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Using a hybrid SARIMA-NARNN Model to Forecast the Numbers of Infected with (COVID-19) in Iraq
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Coronavirus disease (COVID-19) is an acute disease that affects the respiratory system which initially appeared in Wuhan, China. In Feb 2019 the sickness began to spread swiftly throughout the entire planet, causing significant health, social, and economic problems. Time series is an important statistical method used to study and analyze a particular phenomenon, identify its pattern and factors, and use it to predict future values. The main focus of the research is to shed light on the study of SARIMA, NARNN, and hybrid models, expecting that the series comprises both linear and non-linear compounds, and that the ARIMA model can deal with the linear component and the NARNN model can deal with the non-linear component. The models

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