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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 Dec 13 2017
Journal Name
Al-khwarizmi Engineering Journal
Using Activated Carbon developed from Iraqi Date Palm Seeds as Permeable Reactive Barrier for Remediation of Groundwater Contaminated with Copper
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The possibility of using activated carbon developed from date palm seeds wastes as a permeable reactive barrier (PRB) to remove copper from polluted shallow groundwater was investigated. The activated carbon has been developed from date palm seeds by dehydrating methods using concentrated sulfuric acid. Batch tests were performed to characterize the equilibrium sorption properties of new activated carbon in copper-containing aqueous solutions, while the sandy soil (aquifer) was assumed to be inert. Under the studied conditions, the Langmuir isotherm model gives a better fit for the sorption data of copper by activated carbon than other models. At a pilot scale, One-dimensional column experiments were performed, and an integrated model ba

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Publication Date
Tue Aug 01 2017
Journal Name
International Journal Of Scientific & Engineering Research
Integrated System of Information hiding by Applying Three levels
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MB Mahmood, BN Dhannoon

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Publication Date
Sat Sep 01 2018
Journal Name
International Journal Of Renewable Energy Research
Performance of Wind Turbines at Three Sites in Iraq
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Matching between wind site characteristics and wind turbine characteristics for three selected sites in Iraq was carried out. Site-turbine matching for potential wind power application in Iraq has not yet been well reported on. Thus, in this study, five years’ wind speed data for sites located in Baghdad (33.34N, 44.40E), Nasiriyah (31.05N, 46.25E), and Basrah (30.50N, 47.78E) were collected. A full wind energy analysis based on the measured data, Weibull distribution function, and wind turbine characteristics was made. A code developed using MATLAB software was used to analyse the wind energy and wind turbines models. The primary objective was to achieve a standard wind turbine-site matching based on the capacity factor. Another matching

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Publication Date
Tue May 23 2023
Journal Name
Journal Of Engineering
Competitive Adsorption of Three Reactive Dyes by Activated Carbon
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In this study three reactive dyes (blue B, red R and yellow Y) in single , binary and ternary solution were adsorbed by activated carbon AC in equilibrium and kinetic experiments. Surface area, Bulk and real density, and porosity were carried out for the activated carbon.
Batch Experiments of pH (2.5-8.5) and initial concentration (5-100) mg/l were carried out for single solution for each dye. Experiments of adsorbent dosage effect (0.1-1)g per 100 ml were studied as a variable to evaluate uptake% and adsorption capacity for single dyes(5, 10) ppm, binary and ternary (10) ppm of mixture solutions solution of dyes. Langmuir, and Freundlich, models were used as Equilibrium isotherm models for single solution. Extended Langmuir and Freun

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Publication Date
Mon Aug 01 2022
Journal Name
Baghdad Science Journal
The Effect of White Rot Fungus (Ganoderma sp) as Decomposers on Composting Using Combination of Cattle Feces and Water Hyacinth (Eichhornia crassipes) as Organic Matter
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In Indonesia, cattle feces (CF) and water hyacinth (WH) plants are abundant but have not been widely revealed. The use of microorganisms as decomposers in the fermentation process has not been widely applied, so researchers are interested in studying further. This study was to evaluate the effect of the combination of CF with WH on composting by applying white-rot fungal (WRF) (Ganoderma sp) microorganism as a decomposer. A number of six types of treatment compared to R1(ratio of CF:WH)(25%:75%)+WRF; R2(ratio of CF:WH)(50%:50%)+WRF; R3(ratio of CF:WH)(75%:25%)+WRF; R4(ratio of CF:WH)(25%:75%) without WRF; R5(ratio of CF:WH)(50%:50%) without WRF; R6(ratio of CF:WH)

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Publication Date
Wed Aug 11 2021
Journal Name
International Journal Of Pharmaceutical Research
Evaluation of Serum Adropin Levels in Nonalcoholic Fatty Liver Disease as A Complication of Hypothyroidism In Iraqi Patients المؤلفون
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Publication Date
Sat Feb 14 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Assessment of cortisol as salivary psychological stress marker in relation to temporomandibular disorders among a sample of dental students
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Background: University dental students perceived a higher level of stress prior to the final exam associated with raised salivary cortisol levels which could be considered as a useful noninvasive biomarker for measuring acute stress. Using a Helkimo anamnestic and clinical dysfunction scoring for temporomandibular disorders can give a better insight about the association of this marker and temporomandibular joint disorders. The aim of this study was to evaluation level of salivary cortisol in stressor students with temporomandibular disorder and the relation between this marker in relation to temporomandibular disorder severity. This might give a better understanding to the role of psychological stress as an etiological factor for developin

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Publication Date
Thu Dec 01 2016
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
FIRST RECORD OF NIGRA SCALE, PARASAISSETIA NIGRA (NIETNER, 1861) (HEMIPTERA; COCCIDAE) AS A PEST OF FIG TREES IN IRAQ
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     The nigra scale, Parasaissetia nigra (Nietner, 1861) (Hemiptera, Coccidae) recorded as a new insect pest attacking fig trees, Ficus carica (Moraceae) in Iraq. It was observed during April 2014 in residential garden at Al-Hurriyah district in Baghdad.

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Publication Date
Wed Jan 01 2020
Journal Name
Desalination And Water Treatment
Combination of the artificial neural network and advection-dispersion equation for modeling of methylene blue dye removal from aqueous solution using olive stones as reactive bed
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Publication Date
Wed Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
comparison between the methods estimate nonparametric and semiparametric transfer function model in time series the Using simulation
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 The transfer function model the basic concepts in the time series. This model is used in the case of multivariate time series. As for the design of this model, it depends on the available data in the time series and other information in the series so when the representation of the transfer function model depends on the representation of the data In this research, the transfer function has been estimated using the style nonparametric represented in two method  local linear regression and cubic smoothing spline method The method of semi-parametric represented use semiparametric single index model, With four proposals, , That the goal of this research is comparing the capabilities of the above mentioned m

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