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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
Tue Oct 08 2002
Journal Name
Iraqi Journal Of Laser
Study of Laser Propagation Parameters in the Underdense Plasma Region Using a Two Dimensional Simulation Code
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The propagation of laser beam in the underdense deuterium plasma has been studied via computer simulation using the fluid model. An appropriate computer code “HEATER” has been modified and is used for this purpose. The propagation is taken to be in a cylindrical symmetric medium. Different laser wavelengths (1 = 10.6 m, 2 = 1.06 m, and 3 = 0.53 m) with a Gaussian pulse type and 15 ns pulse widths have been considered. Absorption energy and laser flux have been calculated for different plasma and laser parameters. The absorbed laser energy showed maximum for  = 0.53 m. This high absorbitivity was inferred to the effect of the pondermotive force.

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Publication Date
Sun Aug 17 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Pharyngeal airway volume and its relationship to the facial morphology in nasal breathing and mouth breathing subjects (A comparative computerized tomography study)
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Background: The value of lateral cephalometric radiographs to evaluate the pharyngeal airway is limited because it provided 2-dimensional (2D) images of complex 3-dimensional (3D) anatomic structures. Three dimensional analyses of the airway volumes are required to understand oral and pharyngeal adaptations in mouth breathing and nasal breathing subjects. The aim of this study was to measure the pharyngeal airway volume and the size of the face, then compare between pharyngeal airway volume in mouth breathing and nasal breathing subjects and find the gender difference in each group, also to study the relation between pharyngeal airway volume and the size of the face. Material and Methods: Fifty patients including 28 males and 22 females wit

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Publication Date
Mon Dec 30 2024
Journal Name
Wasit Journal For Pure Sciences
A New Class of Higher Derivatives for Harmonic Univalent Functions Established using a Generalized Fractional Integral Operator
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A new class of higher derivatives  for harmonic univalent functions defined by a generalized fractional integral operator inside an open unit disk E is the aim of this paper.

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Publication Date
Thu Aug 01 2019
Journal Name
Transylvanian Review
POSSIBILITY OF APPLICATION THE BALANCED SCORECARD IN THE IRAQI INDUSTRIAL COMPANIES: A PROPOSED MODEL
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POSSIBILITY OF APPLICATION THE BALANCED SCORECARD IN THE IRAQI INDUSTRIAL COMPANIES: A PROPOSED MODEL

Publication Date
Tue Mar 02 2021
Journal Name
Humanitarian And Natural Sciences Journal
THE LINGUISTIC STRUCTURES OF THE HISTORIANS ALYAQOUBI (284 AH / 897 AD) ARE A MODEL
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The research in the linguistic structures of the historians Al-Yaqoubi is considered a model of the important topics in historical studies in general, given its importance in the lives of peoples due to its connotations and meanings that summarize interpretation, clarification, and prolonged speech, as it includes life meanings with many dimensions, these structures have been used in historical incidents Important, and throughout the different ages, as it can be used to support an opinion, solve problems, prove evidence, increase wisdom, and it needs rich life experiences, and a sound language, to use it, and needs a wide absorptive capacity for the recipient, the research included linguistic structures in the achievement of science , Lingu

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Publication Date
Tue Feb 26 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Return Variation on Investment as a Function for the Difference of Market Share: An Applied Research on a Sample of Private Banks listed in Iraq Stock Exchange (ISX)
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    The research specified with study the relation  between the market share for the sample research banks and the amount of the achieved revenues from the investment, where the  dominated belief  that there potentiality enhancing the revenue on investment with the increase of the banks shares in their markets after their success in achieving rates of successive growth in their sales of sales and to a suitable achieve  market coverage for their products and they have dissemination and suitable  promotion activity, the  market share represented the competition  for the banks, and the markets pay attention to the  market share as a strategic objective and to maintain them also increasi

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Publication Date
Tue Feb 01 2022
Journal Name
Baghdad Science Journal
In Situ Hybridization for Molecular Detection of Human Papilloma Viral 6 / 11 DNA in Adenoctomized Tissues from A group of Iraqi Pediatric Patients
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Among more than 200 different human papilloma viral genotypes, the association of low oncogenic risk-HPV genotypes have been recognized with a variety of oral, oropharyngeal, nasopharyngeal benign tumors as well as non-neoplastic polyposis and papillomas and adenoid hypertrophy. This prospective case- control study aims to determine the rate of DNA detection of HPV genotype 6/11 in nasopharyngeal adeno- tonsillar tissues from a group of patients subjected to adenoctomy for adenoid hypertrophy . A total number of nasopharyngeal adeno-tonsillar tissue specimens from pediatric patients with adenoid hypertrophy were enrolled; 40 nasopharyngeal adeno-tonsillar tissues from patients with adenoid hypertrophy, and 20 normal nasal tissue specimen

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Publication Date
Wed Nov 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Authority control and its role in uniting old arabic authors entries at the Central Library of the University of Baghdad and the Al-Mustansiriya: A Comparative Study
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The research aims to identify the positives formulation entrances authors depending on the setting retaining the names of the authors of Arab veterans and cons of setting the entrances to Arab authors ancient depending on the nickname by desktop diligence without reference to a setting retaining the potential to benefit other libraries disciple of retaining existing in sober university libraries. Use the survey method and adopted a questionnaire distributed to the research sample consisting of employees working in the libraries in question and the total number of forms that have been distributed (50) form .tousel search phrase conclusions from them .

1-The lack of authority control depends on it to find a

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Publication Date
Sun Apr 03 2022
Journal Name
Iraqi Journal Of Laser
On the use of Aluminium as a plasmonic material in polarization rotators based on a hybrid plasmonic waveguide
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: The Aluminium (Al) material emerged as a plasmonic material in the wavelength ranges from the ultraviolet to the visible bands in different on-chip plasmonic applications. In this paper, we demonstrate the effect of using Al on the electromagnetic (EM) field distribution of a compact hybrid plasmonic waveguide (HPW) acting as a polarization rotator. We compare the performance of Al with other familiar metals that are widely used as plasmonic materials, which are Silver (Ag) and Gold (Au). Furthermore, we study the effect of reducing the geometrical dimensions of the used materials on the EM field distributions inside the HPW and, consequently, on the efficiency of the polarization rotation. We perform the study based o

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Publication Date
Tue Aug 30 2022
Journal Name
Research Journal Of Pharmacy And Technology
Correlation of Angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers with serum GDF-15 in a group of hypertensive Iraqi patients
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The Growth Differentiation Factor -15 (GDF-15) is a member of the transforming growth factor β superfamily. İt represents an example of the stress response cytokines. It's mostly found in cardiac myocytes, adipocytes, macrophages, endothelial cells, and vascular endothelial cells, whether they're generated normally or not. GDF-15 levels have increased and are associated with cardiovascular risk. Aim of the study: To investigate the correlation between angiotensin-converting enzyme (ACE) inhibitors and angiotensin II receptor blockers (ARBs) with the level of plasma GDF-15 in a group of hypertensive patients. Materials and methods: A case-control study involved 90 individuals, 60 hypertensive patients (36 on ACE inhibitors and 24 on ARBs)

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