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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
Fri Jun 28 2024
Journal Name
Arab World English Journal
Cowboy as a Symbol of Individualism: A Pragmatic Analysis of Red Dead Redemption 2
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As cultures are mainly divided into collectivistic and individualistic, members tend to emphasize, through communication, either their position as part of their group or their independence from the group. This emphasis is manifested in using the pragmatic concepts of positive politeness and negative politeness. The present study looks into the reflection of these two cultures in Rockstar’s renowned video game, Red Dead Redemption 2 (2018). It aims at identifying the two cultures as present in the game and showing their significance to its narrative. It fills the gap in the studies of language used within video games as well as its cultural reflections. The study addresses the following question: What are the positive and negative

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Publication Date
Sun Jun 30 2024
Journal Name
Association Of Arab Universities Journal Of Engineering Sciences
The impact of flexibility in the design of educational interior spaces (University of Baghdad Studio as a model) (أثر المرونة في تصميم الفضاءات الداخلية التعليمية (مراسم جامعة بغداد أنموذجا
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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
A study for Bacterial Infection in Acute Diarrhea Patients
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500 samples of diarrhea stool were collected from different ages(less than 1year –upto30years) and for both genders from some patients in (Alwiya hospital for children, Al-kendi, central health public laboratory and some gavernarated labs) period(1/11/2009—1/10/2010). Kinds of bacteria and parasites agents were isolated and identified from patients with diarrhea. Nine species of gram negative bacteria from enterobacteriaceae were isolated, E. coli isolated are the higher ratio 4.8% of all, then Salmonella typhi4.6% while the lowest ratios is Citrobacterfreundii 0.4%, while the other identified species were be among the previous rotios. also Plesomonasshigelloides was isolated which concedride one of the bacterial local studies.many met

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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
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 Dec 01 2022
Journal Name
Al-khwarizmi Engineering Journa
Comparative Study between Activated Carbon and Charcoal for the Development of Latent Fingerprints on Nonporous Surfaces
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For criminal investigations, fingerprints remain the most reliable form of personal identification despite developments in other fields like DNA profiling. The objective of this work is to compare the performance of both commercial charcoal and activated carbon powder derived from the Alhagi plant to reveal latent fingerprints from different non-porous surfaces (cardboard, plain glass, aluminum foil sheet, China Dish, Plastic, and Switch). The effect of three variables on activated carbon production was investigated. These variables were the impregnation ratio (the weight ratio of KOH: dried raw material), the activation temperature, and the activation time. The effect factors were investigated using Central Composite Design (CCD) softwa

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Publication Date
Thu Dec 01 2022
Journal Name
Al-khwarizmi Engineering Journal
Comparative Study between Activated Carbon and Charcoal for the Development of Latent Fingerprints on Nonporous Surfaces
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For criminal investigations, fingerprints remain the most reliable form of personal identification despite developments in other fields like DNA profiling. The objective of this work is to compare the performance of both commercial charcoal and activated carbon powder derived from the Alhagi plant to reveal latent fingerprints from different non-porous surfaces (cardboard, plain glass, aluminum foil sheet, China Dish, Plastic, and Switch). The effect of three variables on activated carbon production was investigated. These variables were the impregnation ratio (the weight ratio of KOH: dried raw material), the activation temperature, and the activation time. The effect factors were investigated using Central Composite Design

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Publication Date
Fri Aug 06 2021
Journal Name
Research Journal Of Pharmacy And Technology
Molecular Detection and Genotyping of Human Herpes Virus 8 in a sample of Iraqi Blood Donors
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Human herpes virus-8 (HHV-8) infection has increased recently in Arabic countries. HHV-8 in healthy persons does not necessarily cause life-threatening infection, and however, it causes a more severe infection among immunocompromised patients. The distribution of HHV-8 genotypes varies according to ethnicity and depends on the geographic region prior rapid development of global travel. A cross sectional prospective study included a hundred healthy blood donor samples with a mean age of (36.60±10.381), 81% were positive for molecular detection of HHV-8 DNA. PCR results for HHV-8 were strongly related with risk factors such as the number of sexual relations, previous surgeries, blood transfusion, dental operation, and the number of b

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Publication Date
Tue Nov 01 2022
Journal Name
Journal Of Engineering
Comparative Study on the Hardness of Mechroha Water Springs
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The vacancy of natural resources is undoubtedly limited by time. The sustainable development principle recommends modern technology for its protection and renewal. This project conducted analyses on two underground water sources in the north of Algeria (Mechroha Province). Besides, the use of the hardness factor and the adoption of the titration method, which is  the determining the concentration of an unknown solution using a known solution concentration, have permitted the characterization of the examples taken and to verify their conformity to the standard required, the results found showed HT=6.66 French degrees (oF) ) for Ain Guilloume water spring in comparison to Ain Messai water spring H

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Publication Date
Fri Oct 10 2025
Journal Name
Journal Of Physical Education
A Comparative Study of Mental Alertness Between Inactive and Active Individuals In Baghdad University Students Aged 18 – 22 Years Old
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