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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 Jul 30 2021
Journal Name
Turkish Online Journal Of Qualitative Inquiry (tojqi)
A Pragmatic Study of the Student-Teacher Relationship in the Dangerous Minds
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Publication Date
Wed Feb 06 2019
Journal Name
Journal Of The College Of Education For Women
The Effect use of the Internet in Academic Libraries A Case Study
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The aim of this research is to show the importance of the effective use
of the internet in academic libraries; to improve the services and to increase
the competence of librarians.
The research has given some recommendations to improve the quality
of services and the need for cooperative network among academic libraries.

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Publication Date
Wed Mar 30 2022
Journal Name
College Of Islamic Sciences
The Holy Totem in Qur’an, a study in the light of sociolinguistics
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The sacred totem is one of the social phenomena that occupied the ideas of researchers, and took up a wide area of ​​their research, and it is one of those phenomena that emerged from one of the translations of the Tabu; Who took a psychological and anthropological analysis   Because it is one of the social practices, and the main focus of it is the human group and its source is religion. Therefore, this research came with demands, the first of which is to give a semantic concept of the Tommy sanctuary, and then the analytical aspect by standing on the sacred things in the Qur’anic text that God Almighty sanctified, and the third requirement is to examine what people have sanctified, as an analysis of the verses that have

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Publication Date
Sat Apr 30 2022
Journal Name
Al-kindy College Medical Journal
Safety profile of immediate post-partum intrauterine device insertion during caesarean delivery – a clinical trial with three years of follow up
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Background Many countries recommend the use of long-acting reversible contraceptive intrauterine device immediately after cesarean delivery. The cesarean delivery rate in Iraqi public hospitals is 32.2% and may reach 85.8% in private hospitals. Immediate post-partum intrauterine device insertion at cesarean is rarely done in Iraq. Objectives To assess the safety and practicality of immediate post-partum intrauterine device insertion during cesarean delivery for family planning and pregnancy spacing in Iraqi women. Subjects and Methods A single arm clinical trial included 150 eligible women who attended Al-‎Elwiyah Maternity Teaching Hospital or Al Hayat Rahibat Hospital for term delivery. A copper intrauterine device was placed in the ute

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Publication Date
Thu Jan 05 2012
Journal Name
مجلة كلية التربية الأساسية/ جامعة بابل / بحوث المؤتمر العلمي الرابع لكلية التربية الأساسية/جامعة بابل 2011 م
THE DYNAMIC EVOLUTION OF THE SHELL NEBULAE BY USING INTERACTING WIND MODEL
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Publication Date
Mon Sep 30 2019
Journal Name
College Of Islamic Sciences
A book in the science of rhyme for the father of conquest Othman bin Jinni ‹v 392 e›: Investigation and study
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This book in our hands is a 'book in the science of rhymes' written by the linguistic and grammatical world 'Othman bin Jenni' 'T 392 AH', and included in it: the concept of rhyme, its characters, movements, and disadvantages, with mention of its ramifications, defining them by definition, clarification and martyrdom poetry, It is concise in size, but it is a book containing a full science in its content.
The study was divided into two parts, the first: the study, and included a study of the author and the author, I talked first about his life, such as his name and origin, and scientific status, and the words of scientists in it, and so on, and secondly: the name of the book, and his percentage, and the time of its composition, etc. I

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Publication Date
Wed Nov 15 2023
Journal Name
Dirasat: Human And Social Sciences
Media Usage for Pope Francesco's Visit to Iraq March 5, 2021 (A Semiotic Study of the Photograph Welcoming Of the Pope)
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Objectives: The research aims to highlight the semiotic approach and apply it to a photograph of the Pope's reception at Baghdad International Airport, published on the page of the Media Office of Iraqi Prime Minister Mustafa Al-Kazemi in the Twitter application, in order to study its components, analyze its contents and clarify its implications, as well as approach the image as a political and media act. Methods: The stages of research were accomplished by "investigation, observation, and analysis", and the dismantling of the composition of the photograph, thus revealing the hidden and hidden aspects, relying on the semiotic approach to analysis. Results: The study showed that the ideas and meanings included in the image in form

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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
האלמנטים המשותפים בשיריהם של משה בן עזרא ואבו פיראס אלחמדני (מחקר השוואתי) Elements common in the poems of Musa son of Izra and Abu Firas al-Hamdani (A comparative study)
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Abstract:

     Musa son of Yaqoob son of Izra, the Spanish poet, linguist, and  philosopher, was born in Granada. He has many poems representing  types of poetry. Also, he had important books, such as "the Poetry of Israel" and "Contemplative Research". He is knowledgeable in both Hebrew and Arabic, because most of his books were written in Arabic and the then translated to Hebrew. It seemed that he was influenced by Arab poets, specifically Abo Firas, and borrowed many issues, such as comparison, repetition, exaggeration, etc. and included them in his poetry.

     All know that Arabic literature clearly influenced Hebrew literature in the Spanish era. Ara

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Publication Date
Mon Jun 15 2020
Journal Name
Al-academy
Religious references to art of miniatures In the Iranian school (Behzad is a model): عبدالرزاق جبار رحيل
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The study examines the religious references of the art of miniatures in the Iranian school "Bahzad model" completed in Iran during the twelfth century AH, according to the controls and characteristics of the authoritative references. The researcher presented the problem of research, its importance, the need for it and its purpose, defined the terms in the research. The theoretical framework came with three investigations. The first topic of the concept of the reference in the field of knowledge, which concluded the most important features of the reference, is that each symbolic existence corresponds to a real existence and symbolic presence is an input to the realization of the reference. The reference then becomes a sign that acts as a

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Publication Date
Tue Dec 24 2024
Journal Name
Malaysian Journal Of Mathematical Sciences
Exploring the Role of Hunting Cooperation, and Fear in a Prey-Predator Model with Two Age Stages
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The aim of this study is to utilize the behavior of a mathematical model consisting of three-species with Lotka Volterra functional response with incorporating of fear and hunting cooperation factors with both juvenile and adult predators. The existence of equilibrium points of the system was discussed the conditions with variables. The behavior of model referred by local stability in nearness of any an equilibrium point and the conditions for the method of approximating the solution has been studied locally. We define a suitable Lyapunov function that covers every element of the nonlinear system and illustrate that it works. The effect of the death factor was observed in some periods, leading to non-stability. To confirm the theore

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