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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
Wed Dec 11 2019
Journal Name
Journal Of The College Of Education For Women
Terrorism and Internal Displacement in Iraq: A Field Study in Baghdad
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    Terrorism is a serious problem for many societies today. This research aims to identify the impact of terrorism and displacement crisis on human security, which was a shock to the Iraqi society in terms of its impact on the psychological, social and economic conditions of the individual, family, and society. The variety of methods of carrying out the terrorist operations that resulted from the phenomenon of human displacement witnessed by Iraq since the middle of 2014. This phenomenon has its demographic, political and social dimensions.

    In order to achieve the goal of this study and the importance of the subject, the social survey method was used by selecting a sample of 200 IDPs in a compou

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Publication Date
Wed Jun 29 2022
Journal Name
College Of Islamic Sciences
Dairy banks and their legal provisions: -A study in Imami jurisprudence
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Abstract

Among the things that have happened and that have emerged from the developments in society is the phenomenon of dairy banks, where institutions collect milk from donating mothers or sellers of milk and benefit from it by sterilizing and selling it.

This topic is considered one of the important topics, as Islam considers breastfeeding as a link as well as parentage, and it has the same genealogy as the spread of sanctity. Therefore, Imamate jurists addressed this topic with research despite its absence in Islamic societies.

The importance of r

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Publication Date
Tue Nov 01 2022
Journal Name
Alustath
Metrical Phonology in Classical English and Arabic Poetry: A Contrastive Study
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One of the prominent goals of Metrical Phonology Theory is providing stress of poetry on the syllable-, the foot-, and the phonological word- levels. Analysing poetry is one of the most prominent and controversial issues for the involved number and types of syllables, feet, and meters are stable in poetry compared to other literary texts. The prosodic seeds of the theory have been planted by Firth (1948) in English, while in Arabic يديهارفلا in the second half of the eighth century (A.D.) has done so. Investigating the metrical structure of poetry has been conducted in various languages, whereas scrutinising the metrical structure of English and Arabic poetry has received little attention. This study aims at capturing the

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Publication Date
Fri Dec 23 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Aspirin Derivatives Exploration: A Review on Comparison Study with Parent Drug
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In recent decades, drug modification is no longer unusual in the pharmaceutical world as living things are evolving in response to environmental changes. A non-steroidal anti-inflammatory drug (NSAID) such as aspirin is a common over-the-counter drug that can be purchased without medical prescription. Aspirin can inhibit the synthesis of prostaglandin by blocking the cyclooxygenase (COX) which contributes to its properties such as anti-inflammatory, antipyretic, antiplatelet and etc. It is also being considered as a chemopreventive agent due to its antithrombotic actions through the COX’s inhibition. However, the prolonged use of aspirin can cause heartburn, ulceration, and gastro-toxicity in children and adults. This review article hi

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Publication Date
Sat Nov 01 2025
Journal Name
Journal Of Language Teaching And Research
Identity Crisis in Diana Abu-Jaber’s Origin: A Pragma-Stylistic Study
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Identity crisis is a dominant literary theme, especially in most Arab women writers’ works. However, it has not been given enough attention from a linguistic point of view. By so doing, the current study intends to fill this gap by analyzing the identity crisis from a pragma-stylistic perspective by examining the writer's style in three purposely selected extracts from Diana Abu-Jaber’s novel Origin (2007). The study aims to examine the identity crisis by using pragmatic and stylistic tools and to explore the effects of Abu-Jaber’s stylistic choices on the readers of her work. To conduct this study, an eclectic model comprising Searle’s speech acts (1979), Brown and Levinson's politeness theory (1987), Leech's model of figur

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Publication Date
Fri Jan 01 2021
Journal Name
Tigris And Euphrates Rivers: Their Environment From Headwaters To Mouth
Ornamental Fishes: A Looming Danger for Inland Fish Diversity of Iraq
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Publication Date
Fri Sep 06 2024
Journal Name
Journal Of Optics
Synthesis of N-A cysteine-capped CdTe QDs for optical biosensing
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In this investigation, water-soluble N-Acetyl Cysteine Capped-Cadmium Telluride QDs (NAC/CdTe nanocrystals), utilizing N-acetyl cysteine as a stabilizer, were prepared to assess their potential in differentiating between DNA extracted from pathogenic bacteria (e.g. Escherichia coli isolated from urine specimen) and intact DNA (extracted from blood of healthy individuals) for biomedical sensing prospective. Following the optical characterization of the synthesized QDs, the XRD analysis illustrated the construction of NAC-CdTe-QDs with a grain size of 7.1 nm. The prepared NAC-CdTe-QDs exhibited higher PL emission features at of 550 nm and UV-Vis absorption peak at 300 nm. Additionally, the energy gap quantified via PL and UV–Vis were 2.2 eV

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Publication Date
Sun Jun 06 2010
Journal Name
Baghdad Science Journal
Charge density distributions for odd-A of 2s-1d shell nuclei
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An analytical expression for the charge density distributions is derived based on the use of occupation numbers of the states and the single particle wave functions of the harmonic oscillator potential with size parameters chosen to reproduce the observed root mean square charge radii for all considered nuclei. The derived expression, which is applicable throughout the whole region of shell nuclei, has been employed in the calculations concerning the charge density distributions for odd- of shell nuclei, such as and nuclei. It is found that introducing an additional parameters, namely and which reflect the difference of the occupation numbers of the states from the prediction of the simple shell model leads to obtain a remarkabl

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Publication Date
Fri Apr 25 2025
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences (ihjpas)
Spectrophotometric Investigations for Simultaneous Analysis of Certain Antibacterial: A Brief Review
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Antibacterial substances belong to a group of compounds that attack dangerous microorganisms. Therefore, killing bacteria or reducing their metabolic activity will lessen their adverse effects on a biological system. They originated from either synthetic materials, microbes, or mold. Many of these medications treat the gram-negative bacteria from the critical precedence group, such as pseudomonas, carbapenem-resistant acinetobacter, and enterobacterales. This study aims to investigate the simultaneous analysis of specific antibacterial spectrophotometrically. The WHO maintains this list of priority infections with antibiotic resistance. Drug combinations in single dosage forms are becoming increasingly popular in the pharmaceutical industry

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Publication Date
Thu Dec 01 2016
Journal Name
2016 Ieee Symposium Series On Computational Intelligence (ssci)
A fusion of time-domain descriptors for improved myoelectric hand control
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