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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 Apr 01 2019
Journal Name
Journal Of Engineering
Removal of Methyl Orange from Aqueous Solutions by Adsorption Using Corn Leaves as Adsorbent Material
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A comparative study was done on the adsorption of methyl orange dye (MO) using non-activated and activated corn leaves with hydrochloric acid as an adsorbent material. Scanning electron microscopy (SEM) and Fourier Transform Infrared spectroscopy (FTIR) were utilized to specify the properties of adsorbent material. The effect of several variables (pH, initial dye concentration, temperature, amount of adsorbent and contact time) on the removal efficiency was studied and the results indicated that the adsorption efficiency increases with the increase in the concentration of dye, adsorbent dosage and contact time, while inversely proportional to the increase in pH and temperature for both the treated and untreated corn leaves. The equi

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Publication Date
Wed Sep 24 2014
Journal Name
International Journal Of Environmental Science And Technology
Removal of copper ions from contaminated groundwater using waste foundry sand as permeable reactive barrier
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Publication Date
Thu Oct 01 2020
Journal Name
Alexandria Engineering Journal
Biodegradation of reactive dyes by some bacteria using response surface methodology as an optimization technique
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Water pollution as a result of contamination with dye-contaminating effluents is a severe issue for water reservoirs, which instigated the study of biodegradation of Reactive Red 195 and Reactive Blue dyes by E. coli and Bacillus sp. The effects of occupation time, solution pH, initial dyes concentrations, biomass loading, and temperature were investigated via batch-system experiments by using the Design of Experiment (DOE) for 2 levels and 5 factors response surface methodology (RSM). The operational conditions used for these factors were optimized using quadratic techniques by reducing the number of experiments. The results revealed that the two types of bacteria had a powerful effect on biodegradable dyes. The regression analysis reveale

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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of Engineering
Determining and Predicting the Water Demand Dynamic System Model Mapping Urban Crawling and Monitoring Using Remote Sensing Techniques and GIS
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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of Engineering
Determining and Predicting the Water Demand Dynamic System Model Mapping Urban Crawling and Monitoring Using Remote Sensing Techniques and GIS
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The problem of rapid population growth is one of the main problems effecting countries of the world the reason for this the growth in different environment areas of life commercial, industrial, social, food and educational. Therefore, this study was conducted on the amount of potable water consumed using two models of the two satellite and aerial images of the Kadhimiya District-block 427 and Al-Shu,laa district-block 450 in Baghdad city for available years in the Secretariat of Baghdad (2005, 2011,2013,2015). Through the characteristics of geographic information systems, which revealed the spatial patterns of urban creep by determining the role and buildings to be created, which appear in the picture for the

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Publication Date
Sun Dec 12 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Possible Protective Effects of Omega 3, Diazepam and their Combination Against Yohimbine-Induced Clonic Seizure in Mice: Comparative Study
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     Yohimbine is actually confirmed in the United States to be utilized for erectile dysfunction; and recently such drug has become commonly used in body-building communities for its presumed lipolytic and sympathomimetic effects. But ingestion of such drug can bring about epileptic neurotoxic effects.

Many antiepileptic drugs can be utilized to counteract myoclonic seizure; furthermore, diazepam can be used to oppose such type of seizure; in addition, surrogate therapeutic options such as omega 3 may also be utilized.  

In this study, twenty-four (24) mice of both sexes weighing 20-25g were randomly-allocated into 4 groups (6 animals each group) as follows: Group I-

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Publication Date
Tue Jun 01 2021
Journal Name
Annals Of The Romanian Society For Cell Biology
Comparative Study of Serum Angiopoietin like Protein-8 and Hyaluronic Acid in Iraqi Hemodialysis Patients with and without T2DM
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The current work was designed to investigate serum angiopoietin like protein-8 and hyaluronic acid among Iraqi hemodialysis patients with and without type 2 diabetes mellitus, and to find relationship between them, as well as if these patients are at risk of kidney fibrosis. Subjects & Methods: in this study, serum samples were obtained from (60) Iraqis patients with end stage renal diseases (ESRD)on hemodialysis (HD) (30 patients with T2DM (G2) and 30 patients withoutT2DM (G3)) in addition to (30) healthy individuals as a control group (G1), their ages ranged from (35-65) years. The patients attended the Al-Yarmouk Teaching Hospital, Baghdad. Results: the results in this study showed a highly a significant elevation inserum angiopoietin li

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Publication Date
Mon May 16 2022
Journal Name
International Journal Of Biomaterials
Histopathological and Biochemical Comparative Study of Copper Oxide Nanoparticles and Copper Sulphate Toxicity in Male Albino Mice Reproductive System
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Copper (Cu) is an essential trace element for the efficient functioning of living organisms. Cu can enter the body in different ways, and when it surpasses the range of biological tolerance, it can have negative consequences. The use of different nanoparticles, especially metal oxide nanoparticles, is increasingly being expanded in the fields of industry and biomedical materials. However, the impact of these nanoparticles on human health is still not completely elucidated. This comparative study was conducted to evaluate the impacts of copper oxide nanoparticles (CuO NPs) and copper sulphate (CuSO4 0.5 (H2O)) on infertility and reproductive function in male albino mice BALB/c. Body weight, the weight of male reproductive organs, mal

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Publication Date
Tue Sep 30 2014
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Study the Feasibility of Alumina for the Adsorption of Metal Ions from Water
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The present work describes the adsorption of Ba2+ and Mg2+ions from aqueous solutions by activated alumina in single and binary system using batch adsorption. The effect of different parameters such as amount of alumina, concentration of metal ions, pH of solution, contact time and agitation speed on the adsorption process was studied. The optimum adsorbent dosage was found to be 0.5 g and 1.5 g for removal of Ba2+ and Mg2+, respectively. The optimum pH, contact time and agitation speed, were found to be pH 6, 2h and 300 rpm, respectively, for removal of both metal ions. The equilibrium data were analyzed by Langmuir and Freundlich isotherm models and the data fitted well to both isotherm modes as indicated by higher correlation of deter

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Publication Date
Fri Feb 15 2019
Journal Name
Route Educational & Social Science Journal
The effect of the 4-H model on self-regulated learning and life skills for female chemistry students in the second intermediate year
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