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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
Sun Sep 02 2012
Journal Name
Baghdad Science Journal
Study of Reactivity Effect on Reactor Power by Using the Neutronic- Thermohydrolic Coupling
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The study deals with reactivity insertion linear and non linear and/or Ramp reactivity expressed as a polynomial in time in the presence of two Feedback mechanisms, using the neutronic-thermohydraulic coupling in order to predict the neutron behavior as a function of time in terms of reactor power. Also, a comparative study has been achieved in the case of the presence of the feedback mechanisms. Insertion of Ramp reactivities in terms of polynomial in time to study the behavior of power and reactivity as a function of time in the presence of two feedback mechanisms (fuel and coolant) has been carried out and the results are displayed as plots, and showed this results corresponding with international results. The present study shows t

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Publication Date
Sun Oct 02 2016
Journal Name
Journal Of Educational And Psychological Researches
The Effect Of Flexible Grouping Strategy And Three Step Interview Strategy On Achievement Of The History Material Among Student Of The First Intermediate Class
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  The research aims to know The Effect Of Flexible Grouping Strategy  and Three Step Interview strategy on achievement of the history material among student of the first literary class, The Researcher used the experimental design of the two experimental groups and the control group and with post test, researcher group (a) represent the experimental group taught according the Flexible Grouping Strategy  , and Division (c) to represent the second experimental group which studied according Three Step Interview strategy and Division (b ) to represent the control group taught in the traditional method, the number of students (99) students of (33) female students in each division. T

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of Optical Communications
Improving the optical link for UVLC using MIMO technique
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Abstract<p>This paper proposed a theoretical treatment to study underwater wireless optical communications (UWOC) system with different modulation schemes by multiple input-multiple output (MIMO) technology in coastal water. MIMO technology provides high-speed data rates with longer distance link. This technique employed to assess the system by BER, Q. factor and data rate under coastal water types. The reliability of the system is examined by the techniques of 1Tx/1Rx, 2Tx/2Rx, 3Tx/3Rx and 4Tx/4Rx. The results shows the proposed technique by MIMO can get the better performance compared with the other techniques in terms of BER. Theoretical results were obtained to compare between PIN and APD </p> ... Show More
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Publication Date
Mon Jun 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Estimation of the average sample size and defective ratio In a finite individualized inspection with a practical application
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The purpose of this research is to find the estimator of the average proportion of defectives based on attribute samples. That have been curtailed either with rejection of a lot finding the kth defective or with acceptance on finding the kth non defective.

The MLE (Maximum likelihood estimator) is derived. And also the ASN in Single Curtailed Sampling has been derived and we obtain a simplified Formula All the Notations needed are explained.

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Publication Date
Mon Nov 24 2025
Journal Name
Al–bahith Al–a'alami
Persuasive Sentimental Method in the Electronic Newspapers of Terrorist Organizations - A research drawn from a Master Degree thesis
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The paper probes into minute identification of the data of the methods followed in the electronic newspapers that aim to promote terrorist organizations like Al Qaeda and ISIS to draw emotional empathy and sympathy with them.
The paper aims at identifying:
How emotional empathy was utilized by terrorists in E-newspapers.
How useful utilizing emotional empathy was in attracting supporters. The sample that is used in the paper is based on the opening articles of E-newspapers that propagate Al Qaeda and ISIS, e.g. (Sawtu el jihad) “The Sound of Fighting in the Name of God”, (Mua’skar el Battar wal Shamikha wal Khansaa) “Camps of Al Battar, Shamika, and Khansaa”, “Inspire” and (Thurwatu el Sanam, Dabiq, and Rumiyah)

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Publication Date
Thu Oct 01 2009
Journal Name
Iraqi Journal Of Physics
The Structural and Optical Properties of Hydrogenated and Nitrogenated a-Si0.1Ge0.9 and a-Si0.1Ge0.9:3% B Thin Films
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It is shown that pure and 3% boron doped a-Si0.1Ge0.9:H and a-Si0.1Ge0.9:N thin films
could be prepared by flash evaporation processes. The hydrogenation and nitrogenation
are very successful in situ after depositing the films. The FT-IR analysis gave all the
known absorbing bonds of hydrogen and nitrogen with Si and Ge.
Our data showed a considerable effect of annealing temperature on the structural and
optical properties of the prepared films. The optical energy gap (Eopt.) of a-Si0.1Ge0.9
samples showed to have significant increase with annealing temperature (Ta) also the
refractive index and the real part of dielectric constant increases with Ta, however the
extinction coefficient and imaginary part of dielect

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Publication Date
Wed Aug 17 2022
Journal Name
Al–bahith Al–a'alami
Women’s Traits In The Iraqi Satirical Television Show ‘State Of Melon’ A Paper Extracted from A Masters Thesis
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The research aims to know the traits or characteristics of woman in terms of her external
appearance, motives for her behavior, feelings, mood and ability.
It, moreover, seeks woman’s relationship with others as it is presented by the Iraqi
satirical television show “ State of Melon “.
The researcher adopted for that survey approach using the method of content analysis
to study the research sample represented by “ State of Melon “ show which was
exposed through the screen of a group of channels:
“Hona Baghdad Satellite Channel, then Asia Satellite Channel, Dijla Satellite Channel,
and UTV Satellite Channel.”For this, the researcher used Margaret Gallagher’s Model to analyze the image of
woman in

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Publication Date
Sat Jul 05 2025
Journal Name
Annals Of Applied Sport Science
Motor Response Time and Biomechanical Factors in Stationary Handball Shooting Accuracy Among University Players
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Background. Handball is a team sport that demands quick reflexes and precise motor skills, particularly in shooting. Players' ability to shoot accurately and swiftly while stationary makes upper limb reaction time crucial for success. Objectives. The research objective is to study the relationship between the motor time of the muscles of the arms and the index of accuracy of shooting from constancy in fourth-stage students in handball. Methods. The researchers used the descriptive method because it is one of the methods used in the research on a sample of students of the fourth stage of the college of Physical Education and Sports Sciences, where the sample consisted of 29 male students from the community of origin, 43 students. Results. Th

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Publication Date
Sun Jun 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
The Organizational Climate Development in the Light of Job Stress Treatment: A Field Study in Governmental Sheltered Accommodation Houses in the Ministry of Labour and Social Affairs
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        Job stress is considered one of the most important obstacles that may appear in the work field. In order to deal with the obstacles and challenges , the idea to deal with job stress has come to address job stress as one of the most important trends that enable organizations to face those challenges through focusing on the role of job stress and the organizational climate of the organization.

       The research deals with two variables: the job stress as an independent variable, and the organizational climate as a dependent one. Each variable includes five sub-dimensions. These dimensions have been involved in an interaction to form

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Publication Date
Thu Jun 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Isotherms and Kinetics Study for Adsorption of Nitrogen from Air using Zeolite Li-LSX to Produce Medical Oxygen
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This research investigates the adsorption isotherm and adsorption kinetics of nitrogen from air using packed bed of Li-LSX zeolite to get medical oxygen. Experiments were carried out to estimate the produced oxygen purity under different operating conditions: input pressure of 0.5 – 2.5 bar, feed flow rate of air of 2 – 10 L.min-1 and packing height of 9-16 cm. The adsorption isotherm was studied at the best conditions of input pressure of 2.5 bar, the height of packing 16 cm, and flow rate 6 Lmin-1 at ambient temperature, at these conditions   the highest purity of oxygen by this system 73.15 vol % of outlet gas was produced. Langmuir isotherm was the best models representing the experimental data., and the m

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