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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 Mar 06 2011
Journal Name
Baghdad Science Journal
Studying of the optical properties of poly (vinyl alcohol) films using Aluminum sulphate as additive by measuring allowed direct transition energy gap
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The change in the optical band gap and optical activation energy have been investigated for pure Poly (vinyl alcohol)and Poly (vinyl alcohol) doped with Aluminum sulphate to proper films from their optical absorption spectra. The absorption spectra were measured in the wave range from (200-700) nm at temperature range (25-140) 0C. The optical band gap (Eg) for allowed direct transition decrease with increase the concentration of Aluminum sulphate. The optical activation energy for allowed direct transition band gap was evaluated using Urbach- edges method. It was found that ?E increases with increasing the concentration of Al2 (SO4)3 and decreases when temperature increases.

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
The Historical Value of Dickens’s A Tale of Two Cities
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In "historical" fiction, characters that never really existed, give expression to the impact of historical events on the people who really did live through them. The result is not history, as an accurate record of actual events, but fiction in which an earlier age is rendered through the personal joys and sufferings of characters. This paper
aims at investigating the historical realities presented in Dickens’s A Tale of Two Cities.

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Publication Date
Thu Jan 20 2022
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
The Homomorphism of Cubic bipolar ideals of a KU-semigroup
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The idea of a homomorphism of a cubic set of a KU-semigroup is studied and the concept of the product between two cubic sets is defined. And then, a new cubic bipolar fuzzy set in this structure is discussed, and some important results are achieved. Also, the product of cubic subsets is discussed and some theorems are proved.

Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
A THEORETICAL VISION OF THE METHODOLOGY OF MATCHING AND CONGRUENCE
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Perhaps the issue of media and the press, especially one of the most common topics that people deliberate and deal with permanently and continuously. An issue of such significance has pushed researchers to put the following question, “Is it possible to live without media?”, “Can people ignore the newspaper, radio, TV, or the other communication means?”

The answer is very simple. It is difficult for civilized society to overtake information, or dispense with circulation, at the individual or collective level. Yet, the question of how to make the media and how it determines its content still requires extensive media experience; and knowledge of the social structure and its relations; and ac

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Publication Date
Mon Apr 01 2019
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness Of A Proposed Program For Developing The Creative Abilities Of The Students At The University Of Tabuk And Its Effect On The Creative Output Of The Neom Project.
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The aim of this study was to measure the effectiveness of a proposed program to develop the creative abilities of the students of Tabuk University and its impact on the creative output of the NEOM project. The sample of the study consisted of (50) university students divided into two groups: an experimental group of 25 students who receive the proposed training program, and control group of (25) students.

 To achieve these objectives, the researcher designed and developed tools to collect the required data, which were verified their validity and reliability.

The descriptive statistics of mean, standard deviations, correlation coefficient, T test for the associated sample were used in the analysis of the results of th

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
IRAQ BETWEEN A CULTURE OF CIVIL SOCIETY AND A CULTURE OF VIOLENCE
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The title takes its realistic connotations with its symbols, slogans and historical extensions in Iraq, also, the repercussions of the organic crisis that afflicted it for almost half a century, especially after the abortion of the July 14 Revolution and the spread of the culture of weapons, violence and death that we are living in Iraq nowadays.

The topic is suitable for critical analytical studies carried out by specialists in scientific and academic research centers and cultural institutions because they have an important feasibility at the strategic cultural level in Iraq, the Middle East and the world.

Research in Iraq has fallen to the extreme and is no longer effective, to the extent that it represents a severe cri

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Publication Date
Sun Apr 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Study and Diagnosis of the Poverty Phenomenon in Rural Areas of Iraq Using the Traditional Method (Crisp)
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Poverty is defined as a low standard of living in the sense that a poor person can not afford a minimum standard of living. The phenomenon of poverty is one of the most serious problems that must be dealt with seriously. This phenomenon has persisted in Iraq for decades because of the harsh economic conditions and unstable security conditions due to the crises it has faced since 2013. This study requires much study and analysis. And rural areas as a special case. In this study, the researcher examined the poverty line as a criterion in estimating the poverty indicators, which include (poverty percentage H, poverty gap PG, poverty intensity PS), based on the continuous social and economic survey data for households in 2014. The ma

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Publication Date
Mon Jun 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
The phenomenon of negative behavior has studied as a social and psychological phenomenon that effect on the performance and life of workers inside and outside the organization. The adoption of this phenomenon is studied in terms of the role of the interna
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The phenomenon of negative behavior has studied as a social and psychological phenomenon that effect on the performance and life of workers inside and outside the organization. The adoption of this phenomenon is studied in terms of the role of the internal environment of the organization in addressing this behavior, being the variables belong to the field of organizational behavior to see the results of those variables on the Iraqi organizations, since the specificities of it differ from the rest of the Arab and foreign environments. Therefore, this study focused on testing the relationship of the internal environment of the organization and its role in addressing the negative behavior of the workers.

thi

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Publication Date
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
Extraction of Iraqi Jasminumsambac (L.)Oil and Study It?s Effect as Antioxidant Agents
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Key words:Jasminumsambac, Volatile oil, Antioxidant.

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Publication Date
Sun Feb 25 2018
Journal Name
Oriental Journal Of Chemistry
Synthesis and Study of Modified Polyvinyl Alcohol Containing Amino acid moieties as Anticancer Agent
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