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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 Jun 03 2020
Journal Name
Political Sciences Journal
Transitional justice: a study of the concept and mechanisms
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The concept of transitional justice is newly emerging, as it was mainly associated with addressing issues of serious breaches and abuses of human rights during conflicts and situations resulting from violence and the use of force in societies that are in the process of democratization, as transitional justice aims primarily to restore civil peace and rebuild institutions The state needs multidimensional justice: a judicial system that achieves the rule of law, corrective restoration of the wounds of the past, and a distributive characteristic of the redistribution of wealth.

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Publication Date
Sun Dec 01 2013
Journal Name
Political Sciences Journal
Yemeni political system: a study of the internal variables
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النظام السياسي اليمني : دراسة في المتغيرات الداخلية

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Publication Date
Thu Jan 01 2015
Journal Name
Political Sciences Journal
Fiscal federalism: a study of the concept and models
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يمثل الأخذ بالنظام الفيدرالي أطاراً تنظيمياً لشكل الدولة و مرحلة تحول مهمة في بنية الدولة العامة في مختلف مجالاتها، فالانتقال من المركزية في أدارة الشؤون العامة للدولة الى النمط الفيدرالي يمثل تحولا بنيوياً وسيكولوجياً ،حيث يكون هنالك توزيع مكاني - عمودي للسلطة والثروة بين الوحدات المكونة للدولة بشكل يختلف كليا عن الحالة المركزية، ونجد صور تنظيمية عديدة تتأسس ضمن اطار الفيدرالية العام ،

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Publication Date
Fri Dec 31 2021
Journal Name
Journal Of Peace For Humanities And Social Sciences Jphsc
The role of the contract Duration in the pre-contract stage " Comparative study"
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Time crosses one of the most important principles that are agreed upon in contracts, because the temporal dimension has a significant impact on all contract provisions and is not limited to a certain group of them. French and Arab legal jurists alike called for this dimension to be given special attention. That is the term of the contract term; To try to limit the temporal elements, clarify their provisions and distinguish between them, but in the Arab world it did not receive the same attention that it received in the West.

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Publication Date
Mon Apr 04 2022
Journal Name
Journal Of Educational And Psychological Researches
The Degree of Implementation of the Coronavirus Prevention Standards (Covid-19) In the Kingdom Of Saudi Arabia (A COMPARATIVE STUDY BETWEEN FAMILIES OF PEOPLE WITH INTELLECTUAL DISABILITIES AND FAMILIES OF ORDINARY PEOPLE)
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The study aims to identify the degree of implementation of the coronavirus prevention standards (covid-19) in the kingdom of Saudi Arabia and compare it with the families of intellectual disabilities. The study population consisted of all families residing in the Kingdom of Saudi Arabia. To achieve the objectives of the research, the analytical descriptive approach was employed. The study sample consisted of (372) families, among them (84) families with intellectual disabilities, and (288) families without intellectual disabilities. They were chosen from the Saudi community according to what is available for collection in a simple random way, using the standard criteria for the prevention of coronavirus (Covid- 19) Prepared by the resear

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Publication Date
Mon Mar 04 2024
Journal Name
Journal Of Emergency Medicine, Trauma And Acute Care
A comparative immunohistochemical expression of cytokeratin 19 in odontogenic keratocyst, dentigerous, and radicular cysts
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Background: Odontogenic cysts are characterized by their sluggish growth and ability to enlarge, primarily affecting the oral and maxillofacial tissues. Timely diagnosis and treatment are crucial to prevent potentially serious consequences. The present study aimed to evaluate and compare the immunohistochemical expression of cytokeratin 19 in the epithelium of odontogenic keratocyst, dentigerous, and radicular cysts.

Methods: This study analyzed forty-five formalin-fixed, paraffin-embedded tissue blocks containing odontogenic cysts. The sample consisted of fifteen odontogenic keratocysts, fifteen dentigerous cysts, and

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Publication Date
Tue Oct 01 2024
Journal Name
Journal Of Physics: Conference Series
A comparative Analytical Investigation of Different Geomagnetic Storms During Solar Cycles 23 and 24
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Abstract<p>In this work, the geomagnetic storms that occurred during solar cycles 23 and 24 were classified based on the value of the Disturbance Storm Time index (Dst), which was considered an indicator of the strength of geomagnetic conditions. The special criterion of Dst >-50 nT was adopted in the classification process of the geomagnetic storms based on the minimum daily value of the Dst-index. The number of geomagnetic storms that occurred during the study period was counted according to the adopted criteria, including moderate storms with (Dst >-50 nT), strong storms with (Dst >-100 nT), severe storms with (Dst >-200 nT), and great storms with (Dst >-350 nT). The statistica</p> ... Show More
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Publication Date
Wed Dec 27 2017
Journal Name
Al-khwarizmi Engineering Journal
A New Approach for Designing Multi Information Management System Using XML Technology
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XML is being incorporated into the foundation of E-business data applications. This paper addresses the problem of the freeform information that stored in any organization and how XML with using this new approach will make the operation of the search very efficient and time consuming. This paper introduces new solution and methodology that has been developed to capture and manage such unstructured freeform information (multi information) depending on the use of XML schema technologies, neural network idea and object oriented relational database, in order to provide a practical solution for efficiently management multi freeform information system.

    

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Requirements of stress tests model and the possibility to apply in Iraqi banks exploratory study of the views of a sample of staff in the central Bank of Iraq .
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Abstract

This research attempt to explain the essential aspects of one important model in management of Bank risks , that is (stress testing) , which increase the concentrate on it resulting the negative affects of Global financial crisis that it accuar in 2008 to study the application possibilities in iraqian banks to enhancing the safety and financial soundness Becuase the classical tools  in Risk management don’t give clear image on Banks ability  in facing risks, hence the Basel committee on Banking supervision focusing in agreement of Basel 2,3 on stress testing when it doing the internal capital adequacy assessment process (ICAAP) .

To achieving the reseach obje

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Publication Date
Wed Jan 16 2019
Journal Name
Applied Physics A
Detecting the thermoplasmonic effect using ellipsometry parameters for self-assembled gold nanoparticles within a polydimethylsiloxane matrix
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