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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
Tue Jul 01 2025
Journal Name
Alexandria Engineering Journal
Impact of dust storms on plant biomass: Model structure and dynamic study
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Publication Date
Wed May 15 2024
Journal Name
International Journal Of Religion
(The Importance of Knowledge and Work in Islamic Thought) A Study of the Stages of Spiritual Purification According to Imam Al-Ghazali
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Science occupies great importance in Islamic thought. Science and learning are considered an essential part of Islamic teachings, and this importance appears in several aspects,Among them is thatScience as a means of understanding religion :Science is a means of understanding the teachings of the Islamic religion. Islam encourages thinking and rational research to understand the Holy Quran and the Sunnah of the Prophet, enabling Muslims to direct their lives and actions in accordance with the directives of their religion,And also to encourageResearch :Islam encourages scientific research and the use of reason in understanding the nature of the universe and God’s signs in it. Muslims are encouraged to study the natural and social s

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Publication Date
Sat Jun 06 2020
Journal Name
Journal Of The College Of Education For Women
Spatial Analysis of Soil Characteristics and its Effect on Determining the Susceptibility of lands of the RasheedRegion: A Study in Soil Geography
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Twelve pends were selected and distributed on three verticals transects paths on the Tigers river in Al Rasheed county.Passing through land covers, that classified and covers the whole region. Based on the 8 Landsat of the year 2015. It was oriental classified by using Erdas 10.2 . The pedons were distributed on the area of each varicty of these classes. the series of soil according of the transect series (DW74,MMg,DMu6 , Df96) respectively were represented P1 , P2 , P3 , P4  .

The second transits series(DM97,MM5,DM96,DF115) respectively were  represented P5 , P6 , P7 , P8  .The third  transits series(DM46,MMg,MF12,MM11) re

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Strategic orientation and its reflection on the Learning organization: Survey study of a sample of Makers decision the Iraqi Ministry of Communications
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The current research focuses on the extent to which the strategic orientation(entrepreneurial orientation, customer orientation, technology orientation, learning orientation, and investment orientation) affects the learning organization (building common vision, systemic thinking, personal dominance, mental models, team learning)The first hypothesis to test the connection relation between research variables and The second hypothesis was to test the relationship between these variables. In order to ascertain the validity of the hypotheses, the research was based on a questionnaire questionnaire prepared according to a number of In addition to building a fifth sub-variable for the strategic orientation (investment orientation) based

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The role of marketing recovery in improving the organization's reputation An applied study of a sample of private bank managers in Baghdad
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This research aims to know and the role of the marketing recovery dimensions in improving the organization's reputation through an exploratory study of private banks in the city of Baghdad. The aim of the research is to define the role of the marketing recovery through its dimensions (compensation, apology, speed of response, assistance and problem solving), in improving the organization's reputation, as the research will attempt to provide a theoretical framework for the dimensions studied through the most important of what researchers presented and then conduct the applied aspect of the research. Data were collected using a questionnaire-based survey consisting of 35 questions and distributed to 110 managers of private banks in

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Publication Date
Tue Sep 23 2025
Journal Name
مجلة اكليل للدراسات الانسانية
The educational counselor in the school and his role in guidance and problem solving: a field study in the city of Baghdad
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Summary: The study focused on the role of the educational counselor in schools, as an integral part of the educational system that faces multiple challenges and difficulties. In this context, the counselor’s role becomes crucial in attempting to reduce or eliminate such difficulties, in addition to guiding students in an appropriate manner. Methodes: The study employed a descriptive field approach, using interviews and direct observation as tools to examine the actual role performed by school counselors. Results: The study concluded with several key findings, most notably the numerous challenges faced by counselors, including students’ negative behaviors, school dropouts, and the limited administrative support for counselors’ work. Fu

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Publication Date
Wed Apr 12 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Synthesis, Characterization and Study Biological Activity of Some New 1, 3, 4-Thiadiazole and Pyrazolone Derivatives Containing Indole Ring
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This work involves synthesis and characterization of some new 1, 3, 4-thiadiazole or pyrazoline derivatives heterocyclic containing indole ring. The new 2-amino-1, 3, 4-thiadiazole derivatives [IV] and [V] a, b were synthesized by cyclization reaction of 2-methyl-1H-indole-carbothiosemicarbazide [III] in H2SO4 acid or by reaction of indole-3-acetic acid or indole-3-butanoic acid with thiosemicarbazide in the presence of phosphorous oxychloride, respectively. Amide derivatives [VI]-[VIII] were synthesized by the reaction equimolar of 2-amino-1, 3, 4-thiadiazoles and (acetyl chloride, benzoyl chloride, anisoyl chloride and heptanoyl chloride) in DMF and pyridine as accepter. The new pyrazolone derivatives [XI] a, b were synthesized from heati

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Publication Date
Wed May 03 2023
Journal Name
Annals Of Medicine & Surgery
Immunohistochemical expression of beta-catenin in ampullary adenocarcinoma: a cross-sectional retrospective study
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Introduction:

Ampullary carcinomas are uncommon malignant tumours of the digestive system, they usually are adenocarcinomas presenting histologically as three types: intestinal, pancreaticobiliary and mixed. β-catenin is a multifunctional protein involved in physiological homoeostasis and intracellular adhesion. Abnormal nuclear accumulation of β-catenin has been described in many malignancies such as colon, breast, liver and others. The relationships between the immunohistochemical expression of β-catenin and the subtype, the grade and the stage of ampullary carcinoma are studied.

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Publication Date
Thu Jan 31 2019
Journal Name
Journal Of The College Of Education For Women
Polygamy in light of societal changes in Iraq (A Field Study in Baghdad)
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The polygamy as a social was known before Islam, has kept Islam on this system after it organized and put his controls and conditions, as justice between wives and the ability to alimony, it was not the purpose of satisfying the instinct of man and enjoyment, but his goal nominal than that, because it addresses problems humanity has goals noble, so the pluralism overlap of the fabric of families belonging to governance and benefits for women and men and society, which leads to increased ties of love between people of the same society and thus increases the cohesion and importance of the topic and its association with financial conditions have emerged as needed so you viewed in the second scientific Conference of the Department social Ser

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Publication Date
Thu Sep 07 2023
Journal Name
Journal Of Language Studies
A Sociolinguistic Study of Selected Iraqi-Arabic Dialects with Reference to TV Series
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The dramatic series on television have a great impact on people’sattitudes towards dialects of language varieties, by relating theconceptual pictures or prototypes presented by series’ characters tothose dialects. This study aims to show the influence of TV series onIraqi university learners’ gender and age in relating positive ornegative semantic qualities to their dialects. To this end, 150 Iraqi EFLlearners have participated in this study to examine their attitudestowards Baghdadi, Mousli and Nasiriya dialects. The data arecollected by Lambert, Hodgson, Gardner, Fillenbaum's (1960)matched guise technique and then labeled by Willmorth’s (1988)subjective reaction test. A structured interview is conducted to supportthe data

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