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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
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of Systemic C-reactive Protein as a Systemic Inflammatory Marker in the Blood for Patients Undergoing Minor Oral Surgical Procedures
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Background: C-reactive protein (CRP) is an acute phase protein that its plasma levels increase after trauma or surgery so it is used as an indicator for the level of inflammation after surgery. The objective of this study is to investigate pre- and post-operative levels of CRP in three types of oral surgical interventions (Apicoectomy, Impaction, and Impacted teeth exposure). Materials and Methods: A total number of (48) healthy individuals aged (20-60) years who needed oral surgical intervention for either (removal of impacted third molars, exposure of an impacted canine, or Apicoectomy). A 4ml venous blood was obtained from each patient at two occasions (pre-operatively at the day of operation and post-operatively after 48 hours), then ce

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Publication Date
Sun Sep 30 2018
Journal Name
الجامعة المستنصرية كلية الإدارة و الاقتصاد
The possibility of adoption of hybrid cloud computing in Iraqi universities : an analytical study using technology acceptance model
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الناصر، عامر عبد الرزاق عبد المحسن والكبيسي، صلاح الدين عواد كريم. 2018. إمكانية تبني الحوسبة السحابية الهجينة في الجامعات العراقية : دراسة تحليلية باستخدام أنموذج القبول التكنولوجي. مجلة الإدا

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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of The Romanian Society For Cell Biology
Molecular study to the fungus Neosetophomasamarorum was isolated from Al Chabaish marsh, South of Iraq
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IA Ali, FK Emran, DF Salloom, Annals of the Romanian Society for Cell Biology, 2021

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Publication Date
Thu Aug 13 2020
Journal Name
Asia Pacific Journal Of Molecular Biology And Biotechnology
The anticancer molecular mechanism of Carnosol in human cervical cancer cells: An in vitro study
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Carnosol, a phenolic diterpene, is one of the effective anticancer agents naturally occurring in rosemary, sage, parsley, and oregano. The chemoresistance problem increased with the routinely used chemotherapy. Therefore, the efforts to find a substitute with safe and low cost have become crucial worldwide. The current study attempts to inspect the anticancer molecular mechanisms of Carnosol on modulating up- and down- regulation of multiple genetic carcinogenesis pathways. The cytotoxicity of Carnosol on Hela cells was evaluated by MTS assay. Flow cytometry was used to assess apoptosis and cell cycle arrest. The apoptotic morphological changes were obvious by dual apoptosis assay. The differential gene expression after treatment wi

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Publication Date
Thu Nov 20 2025
Journal Name
Al–bahith Al–a'alami
Graduate Media Students’ Satisfaction Level in Their Program of Study:  The level of Satisfaction about the Study Programs of the masters of Media students / Case Study of Media faculties’ students at “Yarmouk University,
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The current study is considered a field study to measure the level of satisfaction of the academic programs of Media Masters students. That was accomplished through surveying the attitudes of the students who are enrolled in the faculties of media at the following universities: (Petra University, The Middle East University (MEU), and Al-Yarmouk University). Those students were enrolled in the master’s program within the formal educational system during the second semester of the academic year (2015 – 2016). This survey aims to identify the services, facilities and academic programs provided by the concerned faculties. It, also, aims to identify the public relations, administrative, educational and services aspects of those faculties.

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Publication Date
Thu Aug 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
Building the optimal portfolio for stock using multi-objective genetic algorithm - comparative analytical research in the Iraqi stock market
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Abstract:

The main objective of the research is to build an optimal investment portfolio of stocks’ listed at the Iraqi Stock Exchange after employing the multi-objective genetic algorithm within the period of time between 1/1/2006 and 1/6/2018 in the light of closing prices (43) companies after the completion of their data and met the conditions of the inspection, as the literature review has supported the diagnosis of the knowledge gap and the identification of deficiencies in the level of experimentation was the current direction of research was to reflect the aspects of the unseen and untreated by other researchers in particular, the missing data and non-reversed pieces the reality of trading at the level of compani

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Publication Date
Sun Dec 31 2023
Journal Name
College Of Islamic Sciences
Imam Al-Mubarakpuri's Jurisprudential Choices (d.1353 AH) in the Borders from his book "Tuhfat Al-Ahwadi" with the explanation of "Jami' Al-Tirmidhi / a comparative jurisprudential study
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Praise be to God, Lord of the Worlds, and prayers and peace be upon the Master of Messengers and his family and companions.

The study of the jurisprudential opinions of scholars, their choices, or their weightings, sheds light on the approach they followed in their choices, and reveals the originality of the scholar or his influence on those who preceded him from among the scholars.

And the commentators of the noble hadith of the Prophet have their important contributions in this aspect, as they undertake the task of explaining the noble hadith, the second source of legislation

Contemporary commentators have their share in the service of the honorable hadith, and the statement of their choices and preferences, and am

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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Engineering
Using of Constructed Wetlands in The Treatment of Wastewater: A Review for Operation and Performance: Review for Using of Constructed Wetlands in The Treatment of Wastewater: Operation and Performance
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Wastewater recycling for non-potable uses has gained significant attention to mitigate the high pressure on freshwater resources. This requires using a sustainable technique to treat natural municipal wastewater as an alternative to conventional methods, especially in arid and semi-arid rural areas. One of the promising techniques applied to satisfy the objective of wastewater reuse is the constructed wetlands (CWs) which have been used extensively in most countries worldwide through the last decades. The present study introduces a significant review of the definition, classification, and components of CWs, identifying the mechanisms controlling the removal process within such units. Vertical, horizontal, and hybrid CWs

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Publication Date
Wed Oct 04 2023
Journal Name
History Of Medicine
Theoretical Biological Activities and Docking studies of new amino-acids Derivatives of Oseltamivir for The Treatment of Coronavirus Disease 2019
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Antiviral medications may be the best choices for COVID-19 treatment until particular therapeutic treatments become available. Tamiflu (oseltamivir) is a neuraminidase inhibitor licensed for the management and defense against influenza types A and B. Oseltamivir-based medication combinations are currently being used to treat COVID-19 patients who also have the new coronavirus 1 SARS-CoV-2. 1 Oseltamivir administration was related with a less time spent in the hospital, quicker recovery 1 and discharge, and a decreased mortality rate. Docking is a modern computational method for identifying a hit molecule by assessing the binding ability of molecular medicines within the binding target pocket. In this work, we chose 21 ligand compounds that

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Publication Date
Wed Sep 29 2021
Journal Name
College Of Islamic Sciences
The provisions of the epidemic in jurisprudence and its principles The (Covid-19) epidemic is a model
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Abstract

Epidemics that afflict humankind are descending renewed, plaguing them in the place and time they spread.

- The epidemic affects individuals and the movement of societies, and its treatment requires dealing with it according to Sharia, taking into account the current data and developments.

- Integrative jurisprudence: it is intended to know the practical legal rulings deduced from the combination of evidence of two or more sciences related to one topic related to it, and among these calamities is the Corona Covid-19 pandemic.

 - It is permissible to use sterile materials that contain a percentage of alcohol in sterilizing hands and fogging places, including mosques.

T

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