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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
Wed Aug 01 2018
Journal Name
Association Of Arab Universities Journal Of Engineering Sciences
Slow sand filtration as a tertiary treatment for the secondary effluent from sewage treatment plant
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A field-pilot scale slow sand filter (SSF) was constructed at Al-Rustamiya Sewage Treatment Plant (STP) in Baghdad city to investigate the removal efficiency in terms of Biochemical Oxygen Demand (BOD5), Chemical oxygen demand (COD), Total Suspended Solids (TSS) and Chloride concentrations for achieving better secondary effluent quality from this treatment plant. The SSF was designed at a 0.2 m/h filtration rate with filter area 1 m2 and total filter depth of 2.3 m. A filter sand media 0.35 mm in size and 1 m depth was supported by 0.2 m layer of gravel of size 5 mm. The secondary effluent from Al-Rustamiya STP was used as the influent to the slow sand filter. The results showed that the removal of BOD5, COD, TSS, and Chloride were

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Publication Date
Thu Jun 01 2023
Journal Name
Medicinal Chemistry
New Niflumic Acid Derivatives as EGFR Inhibitors: Design, Synthesis, In silico Studies, and Anti-proliferative Assessment
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Background:

1,3,4-oxadizole and pyrazole derivatives are very important scaffolds for medicinal chemistry. A literature survey revealed that they possess a wide spectrum of biological activities including anti-inflammatory and antitumor effects.

Objectives:

To describe the synthesis and evaluation of two classes of new niflumic acid (NF) derivatives, the 1,3,4-oxadizole derivatives (compounds 3 and (4A-E) and pyrazole derivatives (compounds 5 and 6), as EGFR tyrosine kinase inhibitors in silico and in vitro.

Methods:

The designed compounds were synthesized using convent

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Publication Date
Mon Feb 28 2022
Journal Name
Journal Of Educational And Psychological Researches
Perceptual for enrolled and not enrolled the puplis in kindergartens (comparative study)
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Enrollment in kindergarten child accomplishes many positive aspects, that’s what Im sure a lot of modern educational trends in child education preschool in the importance of exposing children to a variety of sensory stimuli that contribute to impart a range of sound concepts.

Current research aims to know:

1.the level of sensory perception in the first primary grade students a sample search.

2.differences in perception of elementary first-graders with variable gender male, female))   3.differences in perception of the first primary grade students attending and not attending kindergarten in accordance with variable attendance (attending, not attending).

school students (first grade) from attendi

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison between Methods of Laplace Estimators and the Robust Huber for Estimate parameters logistic regression model
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The logistic regression model regarded as the important regression Models ,where of the most interesting subjects in recent studies due to taking character more advanced in the process of statistical analysis .                                                

The ordinary estimating methods is failed in dealing with data that consist of the presence of outlier values and hence on the absence of such that have undesirable effect on the result.    &nbs

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Publication Date
Tue Mar 30 2021
Journal Name
Baghdad Science Journal
Future of Mathematical Modelling: A Review of COVID-19 Infected Cases Using S-I-R Model
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The spread of novel coronavirus disease (COVID-19) has resulted in chaos around the globe. The infected cases are still increasing, with many countries still showing a trend of growing daily cases. To forecast the trend of active cases, a mathematical model, namely the SIR model was used, to visualize the spread of COVID-19. For this article, the forecast of the spread of the virus in Malaysia has been made, assuming that all Malaysian will eventually be susceptible. With no vaccine and antiviral drug currently developed, the visualization of how the peak of infection (namely flattening the curve) can be reduced to minimize the effect of COVID-19 disease. For Malaysians, let’s ensure to follow the rules and obey the SOP to lower the

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Publication Date
Sun Sep 07 2014
Journal Name
Baghdad Science Journal
Optimum conditions for ascorbic acid determination in three Iraqi citrus using HPLC technique
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A high-performance liquid chromatography method was employed for the quantitative determination of ascorbic acid (AA) which called vitamin C in three types of Iraqi citrus (orange mandarin and aurantium ) and to establish this goal , evaluation of ascorbic acid degradation is so important due to its significant criticality when exposure to ordinary atmospheric conditions. The chromatographic analysis of AA was carried out after their sequential elution with KH2PO4 ( as mobile phase) by reverse-phase HPLC technique with C8 column and UV detection at 214 nm. .Bad resolutions was appeared clearly for C8 column , so another alternative condition were carried out to improve the resolution by replacement of C8 by C18 column .Statistical treat

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Publication Date
Mon Oct 19 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
The effect of using the interactive video accompanying the static training in learning some basic skills of a model school in squash
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Lately great interests have emerged to find educational alternatives to teach and improve motor skills according to modern educational methods that take into account individual differences and speed in learning for the learner through individual learning that the learner adopts by teaching himself by passing through various educational situations to acquire skills and information in the way he is The learner is the focus of the educational process and among these alternatives the interactive video, the researchers noted through the educational training units at the Model Squash School of the Central Union, and that most of the methods and methods used in learning basic skills take a lot of time in the educational program and do not involve

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Publication Date
Mon Oct 02 2023
Journal Name
Journal Of Polymer Research
Morphological study of porous aromatic schiff bases as a highly effective carbon dioxide storages
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Carbon dioxide (CO2) capture and storage is a critical issue for mitigating climate change. Porous aromatic Schiff base complexes have emerged as a promising class of materials for CO2 capture due to their high surface area, porosity, and stability. In this study, we investigate the potential of Schiff base complexes as an effective media for CO2 storage. We review the synthesis and characterization of porous aromatic Schiff bases materials complexes and examine their CO2 sorption properties. We find that Schiff base complexes exhibit high CO2 adsorption capacity and selectivity, making them a promising candidate for use in carbon capture applications. Moreover, we investigate the effect of various parameters such as temperature, and pressu

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Publication Date
Sat Jan 01 2022
Journal Name
International Journal Of Research In Social Sciences & Humanities
Staging Violence in Sarah Kane’s Blasted & Ali Abdulnebi al Ziadi’s Fourth Generation: a Comparative Study
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Violence occurs as a daily human action all over the world; it may cause so many kinds of damage to individuals as well as to society: physical, psychological, or both. Many literary authors of different genres have tried their best to portray violence by showing its negative effects, especially playwrights because they have the chance to show people the dangers of violence through performance on stage to warn them against such negatively affected action. It has been a human action since the beginning of human life on this planet when the first crime happened on earth when Cane killed his brother Abel. In our modern world, people are witnessing daily violent actions as a result of destructive wars that turned the humans into brutal beings.

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Educational And Psychological Researches
Evaluating Educational Programs in Combating Indecent Behaviors Among University Students Using Structural Equation Modeling (Field study: Northern Border University)
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The study aimed to evaluate educational programs efficiency in applying the best educational practices to educate students from the dangers of indecent behaviors, in line with higher education policy and the appropriateness of educational program dimensions to spread awareness among students to not fall into the indecent behaviors clutches. The study adopted the inductive exploratory approach through structural equation modeling and the descriptive analysis of the collected data from randomly selected sample (n=385) from educational academics at Northern Border University in the Saudi Arabia using a specially designed survey tool to meet study purposes to evaluate dimensions of teaching methods, evaluation tools, training courses, course

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