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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
Sun Nov 23 2025
Journal Name
Journal Of Physical Education
Analytical Study of Goalkeeper Positioning Using MH System for Free Kick in Soccer
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Publication Date
Wed Aug 30 2023
Journal Name
Al-kindy College Medical Journal
The Impact of using the Internet and Social Media on Sleep in a group of Secondary School Students from Baghdad
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Background: Insufficient sleep due to excessive media use is linked to decrease physical activity, poor nutrition, obesity, and decreased overall health-related quality of life.

Objectives: To assess the effect of using the internet and social media on the sleep of 4th-stage secondary school students.

Subjects and Methods: Cross-sectional study with the analytic element; for 500 secondary school students, obtained by choosing two schools randomly from each of the six educational directorates, by using a structured questionnaire.

Result: Secondary scho

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Publication Date
Sat Jan 01 2022
Journal Name
The International Journal Of Nonlinear Analysis And Applications
Developing Bulk Arrival Queuing Models with Constant Batch Policy Under Uncertainty Data Using (0-1) Variables
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This paper delves into some significant performance measures (PMs) of a bulk arrival queueing system with constant batch size b, according to arrival rates and service rates being fuzzy parameters. The bulk arrival queuing system deals with observation arrival into the queuing system as a constant group size before allowing individual customers entering to the service. This leads to obtaining a new tool with the aid of generating function methods. The corresponding traditional bulk queueing system model is more convenient under an uncertain environment. The α-cut approach is applied with the conventional Zadeh's extension principle (ZEP) to transform the triangular membership functions (Mem. Fs) fuzzy queues into a family of conventional b

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Publication Date
Fri Jan 01 2021
Journal Name
Chemical Science
Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step
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Fluorescent proteins (FPs) have revolutionised the life sciences, but the chromophore maturation mechanism is still not fully understood. Here we photochemically trap maturation at a crucial stage and structurally characterise the intermediate.

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
LOCAL NEWS SOURCES IN THE IRAQI NEWSPAPERS: Local news sources in the Iraqi newspapers (An analytical study of local news sources In the newspaper Al-Zaman for the period from 1/6/2006 to 06/30/2006)
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Local news is an important topic of the press because of its importance to readers. It touches their daily life in one way or another, which makes them interested in and followers of them. Hence the importance of local news, as it interests a wide segment of readers.
There are many sources of newspapers for obtaining local news, as these sources are distributed to the newspaper's own sources and external sources.

Self-sources are the newspaper's own sources, through which it is possible to obtain this news, such as the representatives of the newspaper and its correspondents and the journalists working in it. This is the example in this way.
The external sources are distributed to local and international news agencies and sa

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Publication Date
Fri Nov 15 2024
Journal Name
Iraqi Journal Of Science
Comparative Analysis for the Seasonal Variations of the IF2 and T Ionospheric Indices during Solar Cycles 23 and 24
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In this work, a comparative analysis for the behavior and pattern of the variations of the IF2 and T Ionospheric indices was conducted for the minimum and maximum years of solar cycles 23 and 24. Also, the correlative relationship between the two ionospheric indices was examined for the seasonal periods spanning from August 1996 to November 2008 for solar cycle 23 and from December 2008 to November 2019 for solar cycle 24. Statistical calculations were performed to compare predicted values with observed values for the selected indices during the tested timeframes. The study's findings revealed that the behavior of the examined indices exhibited almost similar variations throughout the studied timeframe. The seasonal variations were

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Publication Date
Thu Jan 30 2020
Journal Name
Al-kindy College Medical Journal
Accuracy of Fine Needle Aspiration Biopsy (F.N.A.B) in Diagnosis of Breast Lump
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Background: Breast cancer is the first one among Iraqi females. Most of them present later for diagnosis. Early detection center in tertiary hospital practice uses FNAB for early diagnosis. Publications on accuracy of this detection are scarce.

Objective:  To test the accuracy of FNAB in breast lump diagnosis.

Methods: Diagnostic test accuracy study, on 204 women with breast lump, attending the oncology department in 2017.

Results: Fine-needle aspiration biopsy diagnosis of histologically malignant cases were, malignant in 89 (87.3%), suspicious of malignancy in 5 (4.9%), and benign in 4 (3.9%). Complete sensitivity was 87.3%, and specificity

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Publication Date
Sun Mar 19 2023
Journal Name
Journal Of Educational And Psychological Researches
The Effect of Using the Generative Learning Model on the Achievement of First-Grade Intermediate Students of Chemical Concepts in Science
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Abstract

The current research aims to identify the effect of using a model of generative learning in the achievement of first-middle students of chemical concepts in science. The researcher adopted the null hypothesis, which is there is no statistically significant difference at the level (0.05) between the mean scores of the experimental group who study using the generative learning model and the average scores of the control group who study using the traditional method in the chemical concepts achievement test. The research consisted of (200) students of the first intermediate at Al-Farqadin Intermediate School for Boys affiliated with the Directorate of General Education in Baghdad Governorate / Al-Karkh 3 wit

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Publication Date
Sun Jan 01 2023
Journal Name
Revista Iberoamericana De Psicología Del Ejercicio Y El Deporte
THE IMPACT OF ENGINEERING ANXIETY ON STUDENTS: A COMPREHENSIVE STUDY IN THE FIELDS OF SPORT, ECONOMICS, AND TEACHING METHODS
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Publication Date
Thu Mar 25 2021
Journal Name
Modern Sport
The effect of physical exertion training using a vertimax device in developing the characteristic strength with speed and the skill of shooting by jumping in front - high with the hand ball for youth
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The research problem has crystallized and in light of these capabilities, the level of performance depends on the application of modern training methods based on actual experimentation, and those methods aim to develop the components of achievement in this competition, including the quantities of exerting the distinctive strength with speed for the arms and feet, which reflects on good skillful performance because the skill of shooting by jumping forward and high forms A major role in achieving goals during the competition that qualifies the team to win, and through the follow-up of the researcher in the field and academic field, I noticed that there is a weakness in some physical abilities, which affects performance and skill level

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