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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
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
A field study of the problems of queues at some checkpoints in the city of Baghdad
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Abstract

Due to the momentum of winning in the streets of the city of Baghdad as a result of the large number of checkpoints so felt researcher to conduct a field visit to find out the main reasons that led to this congestion and to find practical solutions to mitigate wastage winning the arrival time citizen to where you want the least possible time.

This research aims to overcome the difficulties experienced by citizens to reach their places of work and reduce waste at the time of service and waiting time as well as reduce the cost of waiting.

Has emerged study a set of conclusions, including the use of model queue (G / G / C) and the mome

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Publication Date
Sat Dec 28 2024
Journal Name
Journal Of Physical Education
The Effect of the (Team - Pair - Solo) Strategy in Learning the Accuracy of the Spiking Skill in Volleyball
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This study aims to prepare educational sessions for the strategy (team-pair-solo) in practical volleyball lessons for female students and identifying its effect on learning the accuracy of the spiking skill in volleyball. An experimental design with experimental and control groups was employed on a purposive sample of (30) female students who were to constitute (42.254%) from their community represented by the sophomores at the College of Physical Education and Sports Sciences for Girls / University of Baghdad who are in good standing in the morning study for the academic year (2022-2023), whose total number is (71) students. According to the determinants of the experimental design, participants were divided into two equal groups, a

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Publication Date
Sat Jan 02 2021
Journal Name
The International Journal Of Nonlinear Analysis And Application
Atan regularized for the high dimensional Poisson regression model
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Variable selection in Poisson regression with high dimensional data has been widely used in recent years. we proposed in this paper using a penalty function that depends on a function named a penalty. An Atan estimator was compared with Lasso and adaptive lasso. A simulation and application show that an Atan estimator has the advantage in the estimation of coefficient and variables selection.

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Publication Date
Wed Oct 24 2018
Journal Name
Chemistry Of Materials
Oxidant or Catalyst for Oxidation? A Study of How Structure and Disorder Change the Selectivity for Direct versus Catalytic Oxidation Mediated by Manganese(III,IV) Oxides
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Structure type and disorder have become important questions in catalyst design, with the most active catalysts often noted to be “disordered” or “amorphous” in nature. To quantify the effects of disorder and structure type systematically, a test set of manganese(III,IV) oxides was developed and their reactivity as oxidants and catalysts tested against three substrates: methylene blue, hydrogen peroxide, and water. We find that disorder destabilizes the materialsthermodynamically, making them stronger chemical oxidantsbut not necessarily better catalysts. For the disproportionation of H2O2 and the oxidative decomposition of methylene blue, MnOx-mediated direct oxidation competes with catalytically mediated oxidation, making the most

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Publication Date
Sat Sep 16 2023
Journal Name
مجلة الدراسات المستدامة
A Review Article: Use of fertilizers and their gradual release of mineral nutrients as a remedy to this problem have an adverse environmental impact.
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Throughout Agriculture has mostly relied on the use of natural fertilizers throughout human history, which are compounds that increase the nitrogen levels in the soil. Modern agriculture was made possible by the introduction of synthetic fertilizers at the end of the 19th centuryproduction of agriculture. Their application enhanced crop yields and sparked an agricultural revolution unlike anything the world had ever seen.In the near future, synthetic fertilizers are anticipated to continue to have a significant impa ct on human life, both positively and negatively. They are frequently utilized for producing all t ypes of crops and are essential to plant growth. The significance of synthetic fertilizers is their ability to provide the soil w

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Publication Date
Sat Dec 17 2022
Journal Name
Journal Of The College Of Languages (jcl)
The Use of the Definite article in the Ottoman Turkish Language in the Fourteenth and Seventeenth Centuries: Qaboos Namah and Mazaki Collection as a Model: '' Kabusnâme ve Mezâkî Divanı Örneğinde ''14. ve 17. Yüzyılarda Osmanlı Türkçesinde Harf-i Ta'rifin Kullanması Üzerine Bir İnceleme
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The Turks used the Ottoman Turkish language from the thirteenth century to the twentieth century.  During this period and under the influence of Islamic civilization, a large number of words and structures were used from the Arabic and Persian languages, Therefore, many Arabic grammatical structures were used in the Ottoman Turkish language, such as the definite article simply because it was widely used.

The paper is concerned with the use of the Arabic definite article in the Ottoman Turkish language, and the aim of this contrastive study is to find out the similarities and differences between the two languages ​​in terms of meaning and structure. Since linguistic studies depend on the practical side or applied approach, two

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Publication Date
Wed Sep 01 2021
Journal Name
Baghdad Science Journal
Fuzzy-assignment Model by Using Linguistic Variables
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      This work addressed the assignment problem (AP) based on fuzzy costs, where the objective, in this study, is to minimize the cost. A triangular, or trapezoidal, fuzzy numbers were assigned for each fuzzy cost. In addition, the assignment models were applied on linguistic variables which were initially converted to quantitative fuzzy data by using the Yager’sorankingi method. The paper results have showed that the quantitative date have a considerable effect when considered in fuzzy-mathematic models.

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Publication Date
Fri Aug 15 2025
Journal Name
Albahith Alalami
Tendencies of Scientific Research in the Specialized Journalism the Media Researcher Magazine A survey study
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Publication Date
Sat Apr 29 2023
Journal Name
Research Journal Of Pharmacy And Technology
The Wound Healing effect of the Green Synthesized Iron Oxide Nanoparticles: A Study on Mice
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The extract of fig fruit has shown significant medical usefulness in various fields. The entrance of nanotechnology into the field of medicinal and pharmacology has shown remarkable advantages. Plants contain diverse molecules thatcan reduce metals, and provide a safe, eco-friendly approach for synthesizing nanoparticles. Iron oxide nanoparticles (IONPs) have been reported to possess an antimicrobial effect against some strains of bacteria and moulds. We have aimed to synthesize IONPs from fig fruit extract and investigate the influence of fig extract and IONPs in wound healing of mice. UV-Vis spectroscopy, X-ray diffraction (XRD), and field emission scanning electron microscopy were used to characterize the IONPs that were produced

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Publication Date
Sun Jun 30 2013
Journal Name
College Of Islamic Sciences
ا Hadiths prohibiting the intimidation of a Muslim in the six books - an analytical study
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This research deals with the hadiths of intimidation. An analytical study of the serious effects of intimidation in society. Intimidation and intimidation of a Muslim is a serious matter, because of the anxiety, intimidation, and dispossession of others ’rights, but some consider it easy, and others intimidate jokingly or seriously, which may lead to such intimidation to have effects Serious.
For intimidation entails the death of the individual, the disappearance of his mind, or the loss of his money, etc., from here the need was urgent; to show the vision of the prophetic Sunnah in denouncing intimidation, so we had this humble research tagged with (hadiths prohibiting the intimidation of a Muslim in the books The six are an analyt

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