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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
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
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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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
Tue Jun 15 2021
Journal Name
Al-academy
The impact of the Arab Islamic environment on contemporary painting" The artist Abdul Rahman Al-Suleiman as a model".: محمود حسين عبد الرحمن
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  This research means a study (the impact of the Arab-Islamic environment on contemporary painting, the artist Abd al-Rahman al-Suleiman as a model). The research falls into two axes: the first: the theoretical axis, and the second: the applied axis. The first axis dealt with an introduction that contained: (the research problem, its importance, its goal, its limits, and the definition of terms). This research aims to uncover (the impact of the Arab-Islamic environment on contemporary painting, and the artist Suleiman was a model). And the research limits spatially: Saudi Arabia, and temporally: 2010-2014. This theme included two topics: The first: the characteristics of the Saudi environment and its impact on art. The second: the s

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Publication Date
Tue Jun 14 2022
Journal Name
Chemical Papers
Nile red based dye D–π–A as a promising material for solar cell applications
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A recently reported Nile red (NR) dye conjugated with benzothiadiazole species paves the way for the development of novel organic-based sensitizers used in solar cells whose structures are susceptible to modifications. Thus, six novel NR structures were derived from two previously developed structures in laboratories. In this study, density functional theory (DFT) calculations and time-dependent DFT (TD-DFT) were used to determine the optoelectronic properties of the NR-derived moieties such as absorption spectra. Various linkers were investigated in an attempt to understand the impact of π-linkers on the optoelectronic properties. According to the findings, the presence of furan species led to the planarity of the molecule and a reduction

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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
Mon Nov 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Strategic leadership skills as a moderate of the impact of environmental challenges on effective management of the environment according to the model (VUCA Prime)
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Purpose – The main purpose of this research is to highlight the main role of strategic leadership skills for top managements in accessing to effective management in accordance with the (VUCA Prime) methodology in (VUCA) environment as Miniature virtual environment, which refers to (Volatility), (Uncertainty), (Complexity), and (Ambiguity).

methodology – To achieve the research objective, this study selected the quantitative approach in research design, Questionnaire was used as the main instrument for data collection, the sample comprised the opinion poll (106) individual who functions as a head department. (Structural equation modelling by (Smart Pls3)

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Publication Date
Sun Jan 01 2012
Journal Name
كلية التربية-الجامعة المستنصرية
Study the diffusion of Hydrogen in metals using a Runge-Kutta method
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Publication Date
Mon May 23 2022
Journal Name
The International Journal Of Artificial Organs
Quantitative analysis and control of the torque profile of the upper limb using a kinetic model and motion measurements
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This paper investigates a new approach to the rapid control of an upper limb exoskeleton actuator. We used a mathematical model and motion measurements of a human arm to estimate joint torque as a means to control the exoskeleton’s actuator. The proposed arm model is based on a two-pendulum configuration and is used to obtain instantaneous joint torques which are then passed into control law to regulate the actuator torque. Nine subjects volunteered to take part in the experimental protocol, in which inertial measurement units (IMUs) and a digital goniometer were used to measure and estimate the torque profiles. To validate the control law, a Simscape model was developed to simulate the arm model and control law in which measurem

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