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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
Mon Apr 28 2025
Journal Name
Chemical Papers
New chemiluminometric method for the determination of azithromycin in a continuous flow injection analysis system
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A novel analytical method is developed for the determination of azithromycin. The method utilizes continuous flow injection analysis to enhance the chemiluminescence system of luminol, H2O2, and Cr(III). The method demonstrated a linear dynamic range of 0.001–100 mmol L-1 with a high correlation coefficient (r) of 0.9978, and 0.001–150 mmol L-1 with a correlation coefficient (r) of 0.9769 for the chemiluminescence emission versus azithromycin concentration. The limit of detection (L.O.D.) of the method was found to be 18.725 ng.50 µL−1 based on the stepwise dilution method for the lowest concentration within the linear dynamic range of the calibration graph. The relative standard deviation (R.S.D. %) for n = 6 was less than 1.2%

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Publication Date
Sun Oct 01 2023
Journal Name
Baghdad Science Journal
The Necessary and Sufficient Optimality Conditions for a System of FOCPs with Caputo–Katugampola Derivatives
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The necessary optimality conditions with Lagrange multipliers  are studied and derived for a new class that includes the system of CaputoKatugampola fractional derivatives to the optimal control problems with considering the end time free. The formula for the integral by parts has been proven for the left CaputoKatugampola fractional derivative that contributes to the finding and deriving the necessary optimality conditions. Also, three special cases are obtained, including the study of the necessary optimality conditions when both the final time  and the final state  are fixed. According to convexity assumptions prove that necessary optimality conditions are sufficient optimality conditions.

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Publication Date
Thu Jul 01 2021
Journal Name
Solar Energy
A new approach for employing multiple PCMs in the passive thermal management of photovoltaic modules
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Publication Date
Mon Mar 07 2022
Journal Name
Journal Of Educational And Psychological Researches
The Degree of Focus of The Science Curriculum for the First Intermediate Grade on National, Health, Environmental And Economic Values in Light of the Education Policy in The Kingdom of Saudi Arabia and a Suggested Scenario for a Mechanism to Be Strengthe
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The study aimed to reveal the extent of the first intermediate grade science curriculum focus on the national values, health, environmental, economic values, in the light of the education policy in the Kingdom of Saudi Arabia, in addition to present a proposed vision to strengthen it in the science curriculum for the first intermediate grade. The study was applied to the two books student and the two books of activity on the first-second semesters for the academic year 1441 AH. To analyze the curriculum content, the study used a verified card prepared by the researchers and a criterion for interpreting percentages. The study reached the following results: environmental values ranked first with a concentration of (43%), i.e. with an avera

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Publication Date
Mon Sep 30 2019
Journal Name
College Of Islamic Sciences
What Bukhari shortened to a bug in its attribution: (Applied study in the correct mosque)
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This study aims to show some of Imam Al-Bukhari's criticism of the Hadith from the Metn side, and part of his methodology in dealing with the correct hadiths that are tainted by a bug. This research focuses on what Imam Al-Bukhari summarized in his Sahih illusion of the narrator in his attribution, or uniqueness of the narrator, or to suggest a novel. We find that Bukhari sometimes abbreviates the hadeeth, and does not bring it out completely in his Sahih. He is satisfied with the abbreviated position but has done so because of a bug in it. The Bukhari usually does not declare his intention but knows this through tracking, inspection, and research of the correct hadiths.

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Publication Date
Sat Apr 01 2017
Journal Name
Al–bahith Al–a'alami
Palestinian Media Elite Attitudes towards Recording Cinemas in Addressing the Internal Situations: A Field Study
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The follower of the history of cinema in the world notes that cinema started recording one and these films are varied in their subjects, while the life of man was the material of these films to be in a creative artistic style.
If the Palestinian films produced by Palestinian directors do not have an impact on the local, Arab and international levels, this is due to the weakness in several technical fields or with the intention to make them bad or negligence of those who produce these films.
This research deals with the role played by Palestinian films in dealing with the internal situation from the point of view of the Palestinian media elite in terms of their exposure to films and the motives of this exposure and the expectation

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of The College Of Education For Women
Lying in Arthur Miller's The Crucible: A Pragmatic Study: هديل محمود إبراهيم , جمعه قادر حسين
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Lying is a controversial issue as it is closely related to one's intended meaning to achieve certain pragmatic functions. The use of lying in literary works is closely related to the characters’ pragmatic functions as in the case of Miller's The Crucible where it is used as a deceptive complex phenomenon that cannot be observed out of context. That is, the use of lying as a deceptive phenomenon represents a violation to Grices's Maxims. Thus, the study aims to qualitatively examine the kinds of maxims being violated, the kinds of violations conducted, the strategies followed in the violations, and the pragmatic functions behind such violations across the different categories of lies. To this end, the (30) extracts fou

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Publication Date
Sat Jun 24 2023
Journal Name
Arab World English Journal
Humor in The Stand-Up Comedy You Wanna Hear Something Crazy?: A Universal Pragmatic Study
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Humor is an interesting phenomenon that has been studied widely, yet it is considered a universal trait that cannot be an old subject for a study. This study is conducted to investigate humor from a universal pragmatic lens in a stand-up comedy show, namely, You Wanna Hear Something Crazy?. It aims to study humor as a coin with two sides, the production side and the understanding side. To achieve the aim of the study, the researchers use an eclectic contains Grice’s CP model (1975) and Habermas’s UP model (1979, 1984, 1987, 1998). The study has noted that while using the observance and the non-observance of the cooperative maxims to produce humor, the universal validity claims of truth, sincerity, and normative rightness for rea

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Jalal AL-deen ALhanafi and his educational effect on the IRAQI society - A historical study
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Sheikh Hanafi was born in one of the popular shops of Baghdad with interlocking social relations, and had a profound impact this camp where his talents in the first Venco loving to Mahalah and Baghdad and was born with this development since his days looked forward to the folklore and folk. In the middle of his youth, including authoring loves the heritage of folk legacies began in motion, from Baghdad, books, articles, research has brought him wide acclaim were not possible without the seriousness and diligence, independence and self-Asamath that mushroom on them
The trip was one of his tools in the scientific fame has gone to many Eastern and Asian countries and visited religious and literary institutes and delivered the lectures an

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Publication Date
Sun Oct 07 2012
Journal Name
Journal Of Educational And Psychological Researches
The Participation of the Students of the Colleges of Education in the Iraqi Universities in Literacy and Adult Education in Iraq. The Students of the Departments of Holy Quran and Islamic Education (A model)
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The study focuses on the problem that Iraq is approaching an increasing rate of literacy;the available data refers to a rate of (18% -19%). In addition to the fact that the generalcurrent role of the programs directed to literacy is not actually effective enough to limit the expansion of this rate.

The importance of this study highlights the fact that the Iraqi universities are an important tributary among the tributaries of human development, especially in spreading the education of the voluntary work in literacy field and confirming the connection between the students and their society and their role in solving one of the prominent challenges that face the development, i.e., literacy.

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