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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 Jun 01 2025
Journal Name
Journal Of The College Of Languages (jcl)
Rebellious Self - A Reading in Madame Bovary's Character of Flubert and Hanna Konin by Amos Oz - Comparative study: האני המורדת - קריאה בדמותה של מאדאם בובארי של פלובר וחנה גונן של עמוס עוז – מחקר השוואתי
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The problem of rebellion is considered one of the features of rapid changes that a society undergoes in all spheres and directions of life, especially in the realm of social relations, customs, traditions, values, and principles. Rebellion may manifest itself in rebellion against oneself, against values or traditions, or against social or governmental authority. One may find that submission plays a vital role in all of these interactions. This study deals with the problem of rebellion in the works of two renowned authors: The French Gustave Flaubert and the Israeli Amos Oz, through two main characters who share similar qualities and traits. Emma Bovary and Henna Konin demonstrate this through their rebellion against themselves, their relati

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Publication Date
Sat Jun 25 2022
Journal Name
Al-mağallaẗ Al-šāmilaẗ Li-l-ḥuqūq
The intention to harm others is one of the forms of abuse of the right - a study in the light of American law
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In a world of limited space, the owners are always surrounded by others next to them, and, consequently, there is hardly any activity which the owner may exercise on his land which would not affect the other owners. If he builds a building, that building may block the sun's rays or the air from the buildings next to it and owned by other people. And if he runs a business, the lands adjacent to that business may be overburdened with the accompanying noise or traffic. If oil is prospected in a land, the neighboring lands may be deprived of oil or their owners may be exposed to toxic fumes. Hence the importance of researching the intention of harming others, as it is one of the most important forms of abuse in the use of the right (especially

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Publication Date
Sat Jul 21 2018
Journal Name
The American Society For Virology's 38th Annual Meeting Will Be Held At The University Of Minnesota In Minneapolis, Mn
Comparative Study of different Predators’ effect on Chlorovirus Amplification Foraging on Zoochlorellae-Containing Paramecia?
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Publication Date
Sun Dec 01 2013
Journal Name
Baghdad Science Journal
Assessment of Inflammasome Activity in Type 2 Diabetes Mellitus and Simple Obesity: Comparative Study
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Inflammasome is a multiprotein oligomer complex which is the precursor procaspase-1 and is a component of the innate immune system so that this study aimed to determine the serum levels of interleukin-1? and 18 in patients with T2D and simple obesity in an attempt to clarify the role of inflammasome in these disorders.Twenty five known cases of T2D, twenty four patients with simple obesity and twenty healthy subjects were randomly recruited from AL-Kindy Teaching Hospital in Baghdad to enroll in this study. All the data about the demographic characteristics and anthropometric measurements were determined in all patients, also the C-reactive protein and serum interleukin (IL)-1? and IL-18 levels were obtained from each patient. The results s

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Publication Date
Mon Feb 01 2021
Journal Name
Indonesian Journal Of Electrical Engineering And Computer Science
Comparative study of logistic regression and artificial neural networks on predicting breast cancer cytology
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<p>Currently, breast cancer is one of the most common cancers and a main reason of women death worldwide particularly in<strong> </strong>developing countries such as Iraq. our work aims to predict the type of tumor whether benign or malignant through models that were built using logistic regression and neural networks and we hope it will help doctors in detecting the type of breast tumor. Four models were set using binary logistic regression and two different types of artificial neural networks namely multilayer perceptron MLP and radial basis function RBF. Evaluation of validated and trained models was done using several performance metrics like accuracy, sensitivity, specificity, and AUC (area under receiver ope

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Publication Date
Sat Jan 09 2016
Journal Name
World Journal Of Experimental Biosciences
Comparative study of oral bacterial composition and neutrophil count between smokers and non-smokers
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Publication Date
Wed Mar 30 2022
Journal Name
College Of Islamic Sciences
What the linguists commented on, "I do not know" in the dictionary of Lisan al-Arab, a semantic study
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Absitract

This research was interested in studying the phrase “I don’t know” in the Lisan al-Arab dictionary, and Lisan al-Arab was based on collecting its material from five dictionaries, including: Tahdhib al-Lugha, al-Muqamah, al-Sahih, and the footnotes of Ibn Berri, al-Nihaya and Gharib al-Hadith. The objection to this phrase, and the discussion of its various implications among linguists and the clarification of the closest and most famous content to it according to the data presented to the researcher in his research journey, and to reach this goal, the research division into a preface, five demands and a conclusion and followed the list of sources and references. To define the lexicon of Lisan al-Ar

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Publication Date
Sat Dec 01 2018
Journal Name
Acta Facultatis Medicae Naissensis
The Factors Influencing the Risk of Perforation in Patients with Peptic Ulcers: A Cross-Sectional Study from Central Iraq
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Abstract<p>The aim of this study was to evaluate the risk factors that influence the perforation, regardless of the presence of H. pylori infection, in a sample of Iraqi patients with peptic ulcers, admitted to Al-Kindy Teaching Hospital. A total of 90 patients who had perforated peptic ulcer participated in this study. The diagnosis was based on history, clinical examination, laboratory and radiological investigations and was confirmed intraoperatively. A number of probable risk factors for perforation were investigated. Eighty participants were males and 10 were females (male to female ratio 8:1). About 42.2% of patients were in their fifth decade of life. Forty-nine (54.4%) patients were asymptomatic be</p> ... Show More
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Publication Date
Fri Dec 30 2022
Journal Name
Journal Of The College Of Education For Women
The Death Scene in the "Ayniyah" Poems of Abi Thuayib Al-Huthali and Suda bint Shamardal: A Contrastive Study
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This study is an objective literary study of the poems of Abu Dhu'ayb Al-Hudhali and Su'da Bint Al-Shamrdal. It aims to shed light on the philosophy of death in the poems, and the way this philosophy is treated by both poets. Thus, the main prominent poetic images have been addressed and the outstanding ones have been singled out. The study further investigates the intertextuality with other poetic verses and Quranic verses and reviews the deviation in their semantic, syntactic, and phonetic types. The study adopts the historical approach to examine the occasion of the poems by referring to several historical sources that indicate the seniority. It also adopts the and descriptive-analytical approach represented by the use of content anal

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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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