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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 Dec 23 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Plant-derived Molecules for the Treatment of Tuberculosis: A Review
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Synthetic anti-TB drugs are being used to treat tuberculosis (TB) as they are effective, however, they are accompanied by many side effects. The disease has remained largely uncured till date. The use of plant extracts or phytochemicals along with the anti-TB drugs is a very attractive strategy to make the treatment more effective as phytochemicals have no side-effects, are much less toxic than synthetic anti-TB drugs, are safe to use and most importantly, do not produce resistant strains as opposed to synthetic anti-TB drugs. Approximately 420,000 plant species have been identified globally and among them only a few have been explored for their therapeutic potential. Traditional medicine in different parts of the world has employed crud

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Publication Date
Sat Jun 29 2019
Journal Name
Journal Of The College Of Education For Women
The Repetition in Bushra Al Bustany Poetry: A Stylistic Study
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يعد التكرار من الظواهر الاسلوبية التي اتخذت دورها في بناء النص الشعري الحديث ويقوم على جملة من الاختيارات الاسلوبية لمادة دون أخرى ولصياغة لغوية دون سواها ، مما  يكشف في النهاية عن سرّ ميل هذا النص الشعري أو ذاك لهذا النمط الاسلوبي دون غيره ، وعلى الرغم من ان التكرار يعد مسألة عامة وشائعة في العمل الأدبي ، فأن الاهتمام بهذا الجانب من المنهج الاسلوبي يأتي من جهة كونه مهيمناً له ايحاءاته ودلال

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Publication Date
Sat Dec 30 2023
Journal Name
Journal Of The College Of Education For Women
The Middle East and Contemporary Geostrategic Shifts: A Geopolitical Study
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This research focuses on the contemporary geostrategic transformations that afflicted the countries of the Middle East, with a focus on the countries of the Arab East, after the collapse of the system of international relations, and the emergence of the unipolar system led by the United States of America. After the events of September 11 and the events that followed, especially the occupation of Iraq in 2003, the study area witnessed a group of geopolitical variables and the emergence of dangerous phenomena that threatened the state structure in the countries of the Middle East; the most notably are the phenomenon of terrorism, cross-border armed groups, sectarian polarization, the phenomenon of migration and the internal and the externa

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Publication Date
Tue Feb 10 2026
Journal Name
Al–bahith Al–a'alami
Evaluation in the Kurdish Media Institutions (A Descriptive Study Survey)
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The importance of evaluation depends on many institutions, whether governmental or private, including media institutions, rely on the list to evaluate the weight of things and appreciation, as well as judging things, achievements, and everything related to the institution is concerned. Because through evaluation, institutions can recognize weaknesses and strengths. It is also an effective tool for management review, through which the institution can review everything related to planning and decision-making, leadership, incentives and other administrative matters.

Therefore, this study attempts to shed light on the evaluation process, its basics and its importance in general and in the Kurdish media institutions as a model in part

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Publication Date
Wed Jun 01 2022
Journal Name
Political Sciences Journal
The Middle East and its Strategic Dimensions: a theoretical study
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Characterized the Middle East has geographic, economic, and geostrategic peculiarities, but it suffers from many problems, such as disagreement over what it means as a concept, or what it represents of a geographic extension. The question is related to the ambiguity surrounding the concept of the Middle East? The purpose of its launch? As it relates to its geostrategic, economic, and geo-cultural importance? And manifestations of this importance? And to what extent he retained his value in the strategies of the major powers? Research hypotheses:

-The multiplicity of concepts for the Middle East region, with international political and Geostrategic interests.- The geostrategic value of the Middle East has made it a focal point for

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Publication Date
Tue Dec 27 2022
Journal Name
College Of Islamic Sciences
Verbal joint in the Holy Quran A descriptive analytical study
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The research paper talks about one of the topics that deals with one of the high-style styles in the Holy Qur’an that carries with it a high and influential style in directing the Qur’anic context, as the verses are singled out with certain words, each of which came out to other meanings, which is what was called in the past “what the wording agreed and the meaning differed Or the so-called “faces and analogues” and the meaning of analogues in the language and the Qur’an; To mention a word in a place and it means a meaning other than the other, and to interpret each word with a meaning other than the other meant by the faces, and accordingly the goal of the research is in the linguistic significance, in order to reveal the tr

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Publication Date
Sun May 01 2022
Journal Name
Journal Of Engineering
The Collapsible Soil, Types, Mechanism, and identification: A Review Study
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Collapsible soil has a metastable structure that experiences a large reduction in volume or collapse when wetting. The characteristics of collapsible soil contribute to different problems for infrastructures constructed on its such as cracks and excessive settlement found in buildings, railways channels, bridges, and roads. This paper aims to provide an art review on collapse soil behavior all over the world, type of collapse soil, identification of collapse potential, and factors that affect collapsibility soil. As urban grow in several parts of the world, the collapsible soil will have more get to the water. As a result, there will be an increase in the number of wetting collapse problems, so it's very important to com

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Publication Date
Wed Feb 01 2023
Journal Name
Baghdad Science Journal
Efficient Approach for Solving (2+1) D- Differential Equations
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     In this article, a new efficient approach is presented to solve a type of partial differential equations, such (2+1)-dimensional differential equations non-linear, and nonhomogeneous. The procedure of the new approach is suggested to solve important types of differential equations and get accurate analytic solutions i.e., exact solutions. The effectiveness of the suggested approach based on its properties compared with other approaches has been used to solve this type of differential equations such as the Adomain decomposition method, homotopy perturbation method, homotopy analysis method, and variation iteration method. The advantage of the present method has been illustrated by some examples.

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Publication Date
Sun Jun 03 2012
Journal Name
Baghdad Science Journal
A Biochemical Study for Evaluation and Analysis of Serum Protein of Patients with Different Kidney Tumors
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The amount of protein in the serum depends on the balance between the rate of its synthesis, and that of its catabolism or loss. Abnormal metabolism may result from nutritional deficiency, enzyme deficiency, abnormal secretion of hormones, or the actions of drugs and toxins. Renal cancer is the third most common malignancy of the genitourinary system, and accounts for 3% of adult malignancies globally. Total serum proteins were measured in malignant kidney tumor, benign kidney tumors, and non tumoral kidney diseases patient groups, as well as in healthy individuals. A significant decrease (p< 0.001) of total serum protein levels in patients with malignant kidney tumors when compared with those of benign tumors, non tumoral diseases, and hea

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Publication Date
Fri Aug 28 2020
Journal Name
2 Nd Al-noor International Conference For Science And Technology
Removal of Sulfur Compounds in Iraqi Kerosene Using 1-Ethyl -3- Methyllimidazolium Acetate
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In the present study, 1-ethyl -3-methyllimidazolium acetate ionic liquid is introduced for extractive desulfurization of Iraqi kerosene (1622ppm) and compared with 1-ethyl -3- methyllimidazolium tetrafloroborate. The effect of ionic liquid/ fuel ratio (1/9, 1/4, 1/2), temperature (25, 30,40oC), stirring speed (300,450rpm) and time (10, 30, 90, 180, 360 min) were studied. Sulfur compound analysis was performed using X-Ray fluorescence. The ionic liquid with acetate anion (OAc) showed better performance than tetrafloborate (BF4). The maximum extraction efficiency was 32% achieved at 1/2 IL/Fuel and 40oC after 90min. The oxidation step using hydrogen peroxide (8ml/200ml), catalyzed by acetic acid (2ml) and followed by ionic liquid extraction h

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