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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 Mar 15 2022
Journal Name
Al-academy
The semiotics of the visual image of women in the discourse of empowerment, Saudi Arabia Kingdom as a model
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We studied, in this paper, the semiotics of the visual image of women in the discourse of empowerment, through three models of advertising images expressing the particularities of the Saudi Arabian environment.

We aim to know how the mark operates and how it is interpreted, as a semantic process in which the meaning ranges from description to interpretation, and we studied two hypotheses:

-The advertising image is a structure in which the mark corresponds to the reality and the discourse to the context.

-The significance is not found in the visual sign or in the textual sign of the advertising image, but in the creative event that opens up to the social, cultural, and psychological context, and creates a field of dia

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Publication Date
Sun May 17 2026
Journal Name
Al–bahith Al–a'alami
Media separation: The Relationship of Arab Immigrants with the Media of the Countries of Diaspora (Sweden as a model) (A Research Derived from PhD Dissertation)
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The research seeks to study the subject (Media separation: the Relationship of Arab Immigrants with the Media of the Countries of Diaspora/ Sweden as a model). Where this phenomenon, "problem" has not been subjected to an in-depth study to find out the causes of this media separation and its repercussions on the immigrant, whether in the problem of integration, or his opportunity to work, or adapt to live in the new society.

Separation is a kind of word that is rarely used in Arabic media studies, relevant, sometimes, to the meaning of “refraining from watching TV or listening to the radio or reading newspapers”. Sometimes, it means “not tuning to or using any form of media like radios or newspapers to be updated about what

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Publication Date
Thu Apr 01 2021
Journal Name
Journal Of Molecular Structure
Mixed-ligand complexes of ampicillin derived Schiff base ligand and Nicotinamide: Synthesis, physico-chemical studies, DFT calculation, antibacterial study and molecular docking analysis
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A novel series of mixed-ligand complexes of the type, [ML1(L2)3]Clx [M= Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiff base (HL1) as main ligand, nicotinamide (L2) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL1 was prepared by the interaction of ampicillin drug and 4-chlorobenzophenone. The synthesized mixed ligand complexes were characterized by elemental analysis, UV-Vis, FT-IR,1H-NMR,13C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiff base ligand, HL1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxygen atoms, whereas the sec

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Publication Date
Fri Sep 17 2021
Journal Name
Al-kindy College Medical Journal
Single Layer Extra-Mucosal Versus Double Layer Intestinal Anastomosis for Colostomy Closure: A Prospective Comparative Study
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Background: The main objective was to compare the outcome of single layer interrupted extra-mucosal sutures with that of double layer suturing in the closure of colostomies.

Subjects and Methods: Sixty-seven patients with closure colostomy were assigned in a prospective randomized fashion into either single layer extra-mucosal anastomosis (Group A) or double layer anastomosis (Group B). Primary outcome measures included mean time taken for anastomosis, immediate postoperative complications, and mean duration of hospital stay. Secondary outcome measures assessed the postoperative return of bowel function, and the overall mean cost. Chi-square test and student t-test did the statistical analysis..

Resu

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Publication Date
Mon Apr 03 2023
Journal Name
Chemistryselect
Development and Validation of Spectrophotometric Methods for the Quantitative Determination of Doxycycline Hyclate in Pure Form and Pharmaceutical Formulations Using Flow‐Injection and Batch procedures: A Comparative Study
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Abstract<p>Doxycycline hyclate is an antibiotic drug with a broad‐spectrum activity against a variety of gram‐positive and gram‐negative bacteria and is frequently used as a pharmacological agent and as an effector molecule in an inducible gene expression system. A sensitive, reliable and fast spectrophotometric method for the determination of doxycycline hyclate in pure and pharmaceutical formulations has been developed using flow injection analysis (FIA) and batch procedures. The proposed method is based on the reaction between the chromogenic reagent (V<sup>4+</sup>) and doxycycline hyclate in a neutral medium, resulting in the formation of a yellow compound that shows maximum absorbance at 3</p> ... Show More
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Publication Date
Sun Jun 07 2009
Journal Name
Baghdad Science Journal
The adsorption-desorption process as a method for separation of nitrogen-carbon dioxide gas mixture using activated carbon
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Gas adsorption phenomenon on solid surface has been used as a mean in separation and purification of gas mixture depending on the difference in tendencies of each component in the gas mixture to be adsorbed on the solid surface according to its behaviour. This work concerns to study the possibilities to separate the gas mixture using adsorption-desorption phenomenon on activated carbon. The experimental results exhibit good separation factor at temperature of -40 .

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Publication Date
Mon Aug 01 2022
Journal Name
Baghdad Science Journal
The Patterns of Poisoning Exposure in Different Ages in Duhok Governate: A three Years Study (2016, 2017, 2018)
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Poisoning with toxic substances accidently or deliberately can be life threatening and especially in some countries that lack the essential tests and facilities to identify the types and causes of these toxic substances. In Iraq, as many other countries, poisoning is one of the chronic public health problems. However, very little literature about the pattern of poisoning cases, types and age is available in Duhok Governorate. Therefore, this study was conducted to determine the most common patterns of poisoning and the related age and gender in Duhok Governorate from 2016-2018, which would possibly contribute to the early diagnosis and treatment of poisoning. The present study was conducted for three years, started from 1st of

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Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
A Comparative Study of the Photostabilization of Polyvinyl Chloride with Nano and Micro Nickel Oxide
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NiO nanoparticle synthesis by chemical method and characterized by XRD with crystal size 11.72
nm and grain size 13 nm from FESEM image also NiO micro used ,two NiO as an additive to evaluate the
possibility of producing photodegradable polymers, the practical application of solid-phase photocatalytic
degradation of polyvinyl chloride (PVC- NiO composite films) was investigated. PVC has a negative impact
on the environment since its polymer degrades slowly, yet it has a wide range of industrial applications and
the amount used shows no evidence of diminishing use. Thus, a synthesis of modified PVC- NiO micro and
nano has been studied with 0, 50, 100, 150, 200, 250, and 300 (hours) as irradiation time a

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Publication Date
Sun May 01 2022
Journal Name
Civil Engineering Journal
Phases of Urban Development Impact on the Assessment of Thermal Comfort: A Comparative Environmental Study
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Millions of pilgrims and visitors from numerous parts of the world flock to Karbala (one of the most prominent ideological and religious places in central Iraq) each year to visit the holy shrines in Karbala due to their sanctity. Many improvements have been made to the Two Holy Shrines (THS), the Shrines of Imam Husayn and Imam Abbas, and the area between them (ATHS), due to the high temperatures in this region and to improve pedestrian thermal comfort. Studies on improving outdoor thermal comfort in Karbala are scarce. Hence, this research aims to look into historical and current architectural changes and how they affect thermal comfort. On the hottest summer day, the ENVI-met software program was used to simulate the building des

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Publication Date
Sun May 01 2022
Journal Name
Civil Engineering Journal
Phases of Urban Development Impact on the Assessment of Thermal Comfort: A Comparative Environmental Study
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Millions of pilgrims and visitors from numerous parts of the world flock to Karbala (one of the most prominent ideological and religious places in central Iraq) each year to visit the holy shrines in Karbala due to their sanctity. Many improvements have been made to the Two Holy Shrines (THS), the Shrines of Imam Husayn and Imam Abbas, and the area between them (ATHS), due to the high temperatures in this region and to improve pedestrian thermal comfort. Studies on improving outdoor thermal comfort in Karbala are scarce. Hence, this research aims to look into historical and current architectural changes and how they affect thermal comfort. On the hottest summer day, the ENVI-met software program was used to simulate the building des

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