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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
Thu Oct 18 2018
Journal Name
Al–bahith Al–a'alami
Public exposure to news satellite channels and its relationship to levels of preference and evaluation of programs: Survey study on a sample of the audience of Baghdad City Cente
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The media, especially the satellite channels in our time, are one of the most important pillars of daily life, public and private, for society and people, and are considered by sociologists and sociologists as one of the most important factors of social upbringing and the most important, as a result of the technological and technological development of the media as well as increasing their numbers and vertical and horizontal expansion locally, As well as entering into the lives of individuals and people and leading them to important sites within their interests and preferences, not to mention the long time spent exposure to those media and benefit from the programs offered or broadcast. , The problem of this research is that there is a l

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Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
A Study of the electronic structure of CdS Nanocrystals using density functional theory
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Density Functional Theory at the generalized-gradient approximation level coupled with large unit cell method is used to simulate the electronic structure of (II-VI) zinc-blende cadmium sulfide nanocrystals that have dimensions 2-2.5 nm. The calculated properties include lattice constant, conduction and valence bands width, energy of the highest occupied orbital, energy of the lowest unoccupied orbital, energy gap, density of states etc. Results show that lattice constant and energy gap converge to definite values. However, highest occupied orbital, lowest unoccupied orbital fluctuates indefinitely depending on the shape of the nanocrystal.

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Publication Date
Tue Aug 01 2017
Journal Name
International Journal Of Agriculture And Biology
Molecular Characterization of a Leaf Curl Disease Infecting Zucchini Squash in Iraq
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Publication Date
Mon Jun 01 2020
Journal Name
Iraqi Journal Of Physics
Theoretical Model for Spectroscopic Study of Cu+2, Co+2, and Fe+3 Dissolved in Ethanol with A Different Concentrations
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The absorption spectrum for three types of metal ions in different concentrations has been studying experimentally and theoretically. The examination model is by Gaius model in order to find the best fitting curve and the equation controlled with this behavior. The three metal ions are (Copper chloride Cu+2, Iron chloride Fe+3, and Cobalt chloride Co+2) with different concentrations (10-4, 10-5, 10-6, 10-7) gm/m3. The spectroscopic study included UV-visible and fluorescence spectrum for all different concentrations sample. The results refer to several peaks that appear from the absorption spectrum in the high concentration of all metal ions solution.

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Publication Date
Mon Jan 01 2018
Journal Name
World Journal Of Dentistry
Obturation of Lateral Canals by a New Reciprocating Spreader and a Conventional Finger Spreader by Lateral Condensation Technique: in vitro Comparative Study
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Publication Date
Sat Oct 19 2024
Journal Name
Mustansiriyah Journal Of Sports Science
Traditional Championships sports (Zurkhaneh and Sumo): a comparative historical study of historical origins and traditional rituals
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Many societies have some sports that play a pivotal role in enhancing human physical strength and martial arts and preserving religious values and beliefs. The most prominent of these traditional heroic sports are Zurkhaneh and Sumo, two sports that have their historical origins in the Iranian and Japanese cultural heritage. The research aims at shed light on the historical origins, symbolic rituals, and traditional elements of the sports of Zurkhaneh and Sumo, and to highlight the distinctive characteristics of the sports of Zurkhaneh and Sumo through objective analysis and comparison. The methodology used in this research is the historical approach, using the method of comparative analysis. This method includes analyzing information deriv

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Publication Date
Tue Oct 09 2018
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
A COMPARATIVE HISTOLOGICAL STUDY OF THYROID TISSUE IN CARP FISH CYPRINUS CARPSIO AND MICE SWISS ALBICANS
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    This histological study was carried out to compare between the thyroid gland of mice (as a model of the mammals) and the thyroid tissue of fish.  Unlike mice, the thyroid gland of fish can't be recognized by naked eye.  The present study revealed that the thyroid of mice varied from that of fish by the location and the histological structure. The study classified the physiological state of the thyroid of mice into three states and that of the fish into only two states. Accordingly, the study concluded that the metabolism of thyroid fish was of moderate type.

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Publication Date
Mon Jun 30 2025
Journal Name
Infotech Spectrum: Iraqi Journal Of Data Science
Evaluating AI Language Models in News Retrieval: A Comparative Study Of ChatGPT-Plus and DeepSeek (R1)
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The increasing complexity of how humans interact with and process information has demonstrated significant advancements in Natural Language Processing (NLP), transitioning from task-specific architectures to generalized frameworks applicable across multiple tasks. Despite their success, challenges persist in specialized domains such as translation, where instruction tuning may prioritize fluency over accuracy. Against this backdrop, the present study conducts a comparative evaluation of ChatGPT-Plus and DeepSeek (R1) on a high-fidelity bilingual retrieval-and-translation task. A single standardize prompt directs each model to access the Arabic-language news section of the College of Medicine, University of Baghdad, retrieve the three most r

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Publication Date
Mon Oct 28 2019
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Kinetic profile of silver and zinc oxide nanoparticles by intraperitoneal injection in mice , a comparative study
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Publication Date
Thu Mar 25 2021
Journal Name
International Journal Of Drug Delivery Technology
A comparative study of retinol-binding protein-4 and progranulin in iraqi women with thyroid disorder
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Thyroid hormones (TH) regulate the metabolic processes required for normal development and growth; also, to organizemetabolism in adults, any defect in thyroid function leads to abnormality in thyroid hormones level. The current study hasbeen designed to find the relationship between retinol-binding protein-4 and progranulin in the serum of Iraqi women withhypothyroidism and hyperthyroidism, also, to study whether these patients are exposed to a risk of developing diabetes mellitus,and PGRN may be a biomarker in detection early stage of diabetes mellitus.Materials and Methods: in this study, serum samples were obtained from 50 Iraqis women patients, [25 patients withhypothyroidism (G2) and 25 patients with hyperthyroidism (G3)] in addition

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