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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 Jun 01 2010
Journal Name
Journal Of The College Of Languages (jcl)
Nature of a holy book in the poetry of Ibn Arabi Mohi
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The paper discusses the lack of a uniform definition of politeness due to the constant tension between its universality and language specificity, and argues that some of the theoretical debate could be resolved if the distinction between politeness as a commonsense notion and politeness as a theoretical construct were clearly addressed and acknowledged in the research.

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Publication Date
Fri Mar 12 2021
Journal Name
Alustath Journal For Human And Social Sciences
A Cognitive Stylistic Analysis of Characterization in Golding’s Lord of the Flies
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Characterization is commonly known in stylistics to be the cognitive process in the readers' minds when comprehending a fictional character in a literary work .In one approach, it is assumed that characters are the outcome of the interaction between the words in the text on the one hand and the contents of our heads on the other. This paper is an attempt to understand how characterization is achieved by applying Culpeper’s (2001) model which seems to be to present a method of analysis that is more objective and more systematic in analyzing characters. Two characters are selected for discussion; Ralph and Jack from Golding’s (1954) Lord of the Flies. The novel talks about the corruption of human beings and the capacity of evil th

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Publication Date
Thu May 14 2020
Journal Name
Journal Of Planner And Development
Property ownership and its implications for urban development The Case study (the development project of the Rashid camp for housing in Baghdad)
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        Of the importance of the concept of ownership of real estate as the basic basis from which various projects are launched in various economic, tourism, and urban areas .... The need to research the diagnosis of real estate reality went astray in the difficulties, which played a decisive role in the process of urban development.

 

 This leads us to the research problem of the difficulty of implementing urban development plans in many cases due to the absence of a clear methodology for organizing and modernizing the ownership of real estate and its coordination with the management of urban land and to achieve the objective

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Publication Date
Sat Sep 12 2020
Journal Name
Al-kindy College Medical Journal
A Brief view on the pediatric COVID- 19 pandemic
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The world is currently challenging the serious effects of the pandemic of the Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Data on pediatric COVID are rare and scattered in the literature. In this article, we presented the updated knowledge on the pediatric COVID-19 from different aspects. We hope it will increase the awareness of the pediatricians and health care professionals on this pandemic.

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Publication Date
Sat Apr 08 2023
Journal Name
Iraqi Journal Of Oil And Gas Research (ijogr)
How to Estimate the Major Petrophysical Properties: A Review
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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
Zebra Mussel Dreissena polymorpha a pest infesting the electricity
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The oyster ??????? (planned) (Pallas) of lesions that have entered Iraq recently became spyware severe damage in more than a station from power plants in Iraq, including the power plant in Mussayab Vamahar accumulates in pipes cooling and disrupts their work Vtafrtf heat systems cooling and thereby determiningefficiency and lead to added cost many cleaning or replacement of damaged parts

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Publication Date
Sat Jun 06 2020
Journal Name
Journal Of The College Of Education For Women
The Tribal Power in Contemporary Iraq: A Sociological Analysis
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This is an empirical investigation of the tribal power in Iraq and its consequences on the socio-political system. A theoretical background concerning thestate kinship, tribe and tribal involvement in politics has been displayed with example of tribal power over people within the social context. Socio-anthropological method of data collection has been used, including a semi-structured interview with a sample of 120 correspondents. The outcome revealed that the feeble and corrupted state (government) play a vital role in encouraging the tribe to be dominant. The people of Iraq are clinging to the tribe regardless of whether they believe in it or not. Although they are aware that the tribe is a pre-state organisation and marred shape of ci

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Publication Date
Wed Feb 01 2023
Journal Name
Baghdad Science Journal
A Heuristic Approach to the Consecutive Ones Submatrix Problem
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Given a matrix, the Consecutive Ones Submatrix (C1S) problem which aims to find the permutation of columns that maximizes the number of columns having together only one block of consecutive ones in each row is considered here. A heuristic approach will be suggested to solve the problem. Also, the Consecutive Blocks Minimization (CBM) problem which is related to the consecutive ones submatrix will be considered. The new procedure is proposed to improve the column insertion approach. Then real world and random matrices from the set covering problem will be evaluated and computational results will be highlighted.

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Publication Date
Thu Oct 12 2023
Journal Name
Mustansiriyah Journal Of Pure And Applied Sciences
Cavitation microbubbles in the medical ultrasound imaging: A Review
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Ultrasound is a mechanical energy which can generate altering zones of compression and rarefaction along its path in the tissues. Ultrasound imaging can provide a real time screening for blood and multiple organs to aiding the diagnostic and treatment. However, ultrasound has the potential to deposit energy in the blood and tissues causing bio effects which is depending on ultrasound characteristics that including frequency and the amount of intensity. These bio effects include either a stable cavitation presented non thermal effects or inertial cavitation of harmful effect on the tissues. The non-thermal cavitation can add features in diagnostic imaging and treatment more than the inertial cavitation. Ultrasound Contrast agents are a micro

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Publication Date
Thu May 15 2025
Journal Name
Journal Of Legal And Political Studies
International and Regional Competition in the Middle East and its Impact on Iraqi National Security, with Special Reference to the Kurdistan Region: A Study of Challenges and Opportunities
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This competition between competing forces, organized into axes with conflicting objectives, is reflected in all regional affairs and the goals and interests of countries within them, including Iraq. Among the most important aspects impacted by the repercussions of international and regional competition in the region is Iraqi national security, based on its vital importance in preserving the sovereignty and entity of the Iraqi state, protecting the interests and cohesion of the state and people, ensuring and defending their present and future, and interacting with various regional and international activities. The Kurdistan Region, as an important part of Iraq with its own unique characteristics, may be one of the most important regi

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