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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
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
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
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
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
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
The impact of the integrative role of the Business Intelligence system and Knowledge Conversion Processes in Building a learning organization A field research in Korek telecom company in Baghdad city
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Purpose:  The research aims to explore the impact Business Intelligence System (BIS) and Knowledge Conversion Processes (KCP) in the Building Learning Organization (LO) in KOREK Telecom Company in Baghdad city.

Design/methodology/approach: in order to achieve the objectives of the research has been the development of a questionnaire prepared for this purpose and then has tested the search in the telecommunications sector, representatives of one of the telecommunications companies in Baghdad city, has therefore chosen KOREK Telecom company as a sample for research, and the choice was based on the best standard international companies to serve mobile communications in terms o

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Analysis of financial investments using financial indicators Applied in the Middle East Bank of Iraq for investment For the fiscal period 2007-2009
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The research explain the analysis of finance investments through  analyze the finance tables for commercial banks, by using the pointers to indicate the limits of economical benefit for these investments, and fix the negative deviations and as well positive, for the purpose of  diagnostic the negative (disadvantage) and develop the advantage deviation, For the importance of finance investments in the development operation and economical growth, further to that the finance investments is represent one of the most activities in the commercial banks in which aim the adequate incomes as a result of the commercial banks act to receipt the banks deposits and then make it growth and develop through  commercial advantage o

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of The College Of Languages (jcl)
A comparative reading of the social and political satire in the works of Abu al-Fadl Zrui Nasrabad and Ahmad Rajab (The tadhk: خوانش تطبیقی طنز اجتماعی – سیاسی در آثار ابوالفضل زرویی نصرآباد و احمد رجب(مورد مطالعه: تذکرة المقامات زرویی و نصف كلمة احمد رجب)
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           Satire is genre of the literary arts that has always been the source of human interest. Because  it is difficult to accept direct criticism, Satire appears as a literary tool in which vices, follies, abuses and shortcomings are held up to ridicule, with the intent of shaming individuals, corporations, government, or society itself into improvement. A satirical critic usually employs irony to attain this goal. Although satire is usually meant to be humorous, its greater purpose is often profitable social criticism, using wit to draw at

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