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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 May 29 2019
Journal Name
Iraqi Journal Of Physics
Improvement the efficiency of SnO2/n-Si detector by engraving method using a CNC machine
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Tin oxide was deposited by using vacuum thermal method on silicon wafer engraved by Computer Numerical Controlled (CNC) Machine. The inscription was engraved by diamond-made brine. Deep 0.05 mm in the form of concentric squares. Electrical results in the dark were shown high value of forward current and the high value of the detection factor from 6.42 before engraving to 10.41 after engraving. (I-V) characters in illumination with powers (50, 100, 150, 200, 250) mW/cm2 show Improved properties of the detector, Especially at power (150, 200, 250) mW/cm2. Response improved in rise time from 2.4 μs to 0.72 μs and time of inactivity improved 515.2 μs to 44.2 μs. Sensitivity angle increased at zone from 40o to 65o.

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Publication Date
Mon Feb 02 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of antibacterial action of photosensitizer solution activated by diode lamp and three intracanal medicaments (in vitro study)
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Background: The elimination of the microorganisms from the root canal systems, an important step for the successful root canal treatment. This study was conducted to evaluate the antibacterial effectiveness of the photoactivated disinfection by using the toluidine blue O and a low- energy light emitting diode (LED) lamp . Materials and method: Sixty single rooted extracted teeth were decoronated, instrumented, irrigated, sealed at the apex and contaminated with endodontic anaerobic bacteria for 7 days to form biofilms in prepared root canals. Group I. Twelve teeth were medicated by photosensitizer (toluidine blue O) solution activated by diode lamp (FotoSan; CMS Dental, Copenhagen, Denmark).Group II. Twelve teeth were medicated by the tricr

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Publication Date
Mon Jan 01 2018
Journal Name
The Journal Of Contemporary Dental Practice
Assessment of Ions released from Three Types of Orthodontic Brackets immersed in Different Mouthwashes: An in vitro Study
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Fabricating a new Rheometer for Concrete
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A new concrete rheometer is introduced including its innovation, actual design, working rules,
calibration, and reliability. A modified design of Tattersall two-point device is created. Some of
components are purchased from local and foreign markets, while other components and the
manufacturing process are locally fabricated. The matching viscosity method of determining the mixer
viscometer constants is demonstrated and followed to relate torque and rotational speed to yield stress
and viscosity (Bingham parameters). The calibration procedures and its calculation are explained.
Water is used as a Newtonian fluid, while; cement paste (cement + water) with w/c ratio equal to
(0.442) is used as a non-Newtonian fluid. Th

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Publication Date
Sat Apr 21 2012
Journal Name
Arabian Journal For Science And Engineering
A Procedure for Analysing Reinforced Embankments
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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of Global Pharma Technology
Study of the genetic diversity in three species belonging to family: Daphniidae (Crustaceae, Cladocera) collected from different regions in Baghdad Province/Iraq
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Publication Date
Mon Feb 02 2026
Journal Name
Al Kut Journal Of Economics And Administrative Sciences
Use of the Bootstrap in the logistic regression model for Breast cancer disease
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The logistic regression model is one of the oldest and most common of the regression models, and it is known as one of the statistical methods used to describe and estimate the relationship between a dependent random variable and explanatory random variables. Several methods are used to estimate this model, including the bootstrap method, which is one of the estimation methods that depend on the principle of sampling with return, and is represented by a sample reshaping that includes (n) of the elements drawn by randomly returning from (N) from the original data, It is a computational method used to determine the measure of accuracy to estimate the statistics, and for this reason, this method was used to find more accurate estimates. The ma

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Publication Date
Thu Dec 01 2011
Journal Name
Iraqi Journal Of Physics
Design of Achromatic Combined Quadrupole Lens Using the Modified Bell-Shaped Field Distribution Model
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The optimization calculations are made to find the optimum properties of combined quadrupole lens consist of electrostatic and magnetic lenses to produce achromatic lens. The modified bell-shaped model is used and the calculation is made by solving the equation of motion and finding the transfer matrices in convergence and divergence planes, these matrices are used to find the properties of lens as the magnification and aberrations coefficients. To find the optimum values of chromatic and spherical aberrations coefficients, the effect of both the excitation parameter of the lens (n) and the effective length of the lens into account as effective parameters in the optimization processing

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Publication Date
Mon Jun 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Using the Logistic Regression Model in Studding the Assistant Factors to Diagnose Bladder Cancer
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The cancer is one of the biggest health problems that facing the world . And  the bladder cancer has a special place among the most spread cancers in Arab countries specially in Iraq and Egypt(2) . It is one of the diseases which can be treated and cured if it is diagnosed early . This research is aimed at studying the assistant factors that diagnose bladder cancer such as (patient's age , gender , and other major complains of hematuria , burning or pain during urination and micturition disorders) and then determine which factors are the most effective in the possibility of diagnosing this disease by using the statistical model (logistic regression model) and depending on a random sample of (128) patients . After

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Publication Date
Wed Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison of Bayes Estimators for the parameter of Rayleigh Distribution with Simulation
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   A comparison of double informative and non- informative priors assumed for the parameter of Rayleigh distribution is considered. Three different sets of double priors are included, for a single unknown parameter of Rayleigh distribution. We have assumed three double priors: the square root inverted gamma (SRIG) - the natural conjugate family of priors distribution, the square root inverted gamma – the non-informative distribution, and the natural conjugate family of priors - the non-informative distribution as double priors .The data is generating form three cases from Rayleigh distribution for different samples sizes (small, medium, and large). And Bayes estimators for the parameter is derived under a squared erro

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