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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 Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Uric Acid as a Natural Scavenger of Peroxynitrite in a Sample of Iraqi Patients with Rheumatoid Arthritis
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Rheumatoid arthritis (RA) is a chronic inflammatory disease associated with decreased antioxidant state .This study aim to investigate the status of oxidant/antioxidant in a sample of  Iraqi patients with RA and the role of peroxynitrite and its natural scavenger uric acid in them .This case-controlled study was conducted at Baghdad teaching hospital /Baghdad from December 2010-May 2011 . Twenty-five patients with mean age 39 years and 25 apparently healthy subject as controls with mean age 29 years were included in the study .Investigations include estimation of serum levels of nitric oxide (NO)  ,peroxynitrite (PN) , malondialdehyde (MDA)  , and uric acid (UA) .Serum PN levels were significantly elevated in RA patients a

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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
Thu Sep 10 2020
Journal Name
Journal Of Advances In Mathematics
A Study of The Density Property in Module Theory
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In this paper, there are two main objectives. The first objective is to study the relationship between the density property and some modules in detail, for instance; semisimple and divisible modules. The Addition complement has a good relationship with the density property of the modules as this importance is highlighted by any submodule N of M has an addition complement with Rad(M)=0. The second objective is to clarify the relationship between the density property and the essential submodules with some examples. As an example of this relationship, we studied the torsion-free module and its relationship with the essential submodules in module M.

Publication Date
Thu Dec 31 2015
Journal Name
مجلة كلية العلوم الاسلامية
The Secret of Marriage in Christianity A Descriptive Study
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Marriage is a holly secret in Christian religion .So it id natural that its ceremonies acquired religious form .In general the marriage is contracted by minister of religion in presence of the two parties or by a proxy or presence of parents if it is necessary . And to make the condition of publicity for the marriage ,its procedures must be made before witnesses .Also the minister of religionhave to confirm the agreement of the two parties before beginning the procedures.The marriage ceremonies are made.These procedures are religious traditions that includes praying and make blessings and putting the rings in fingers by thepriest . The marriage is a holly secret performed by the crown pray according to the church religious traditions

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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
Fri Aug 30 2019
Journal Name
Journal Of The College Of Education For Women
A Cognitive Linguistic Study of the English Preposition 'in'
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The present study aims at analyzing the polysemy of the English preposition in from the cognitive linguistic (CL) point of view using Evans' and Tyler's approach (2003). The perplexity faced by Iraqi second language learners (L2) due to the multi-usages of this preposition has motivated the researcher to conduct this study. Seventy-six second year university students participated in this experimental study. The data of the pre-test and post-test were analyzed by SPSS statistical editor. The results have shown the following: First, a progress of more than (0.05≤) has been detected as far as students' understanding of the multiple usages of the preposition in is concerned. Second, the results of the questionnaire have s

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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
Sat Apr 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
Using PCR and Gel Electrophoresis Techniques to Molecular Confirm and Detection for Flowering Gene Presence in Maize Hybrids
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Abstract<p>The laboratory experiment was conducted in the laboratories of the Musayyib Bridge Company for Molecular Analyzes in the year 2021-2022 to study the molecular analysis of the inbreed lines and their hybrids F1 to estimate the genetic variation at the level of DNA shown by the selected pure inbreed lines and the resulting hybrids F1 of the flowering gene. Five pure inbreed lines of maize were selected (ZA17WR) Late, ZM74, Late, ZM19, Early ZM49WZ (Zi17WZ, Late, ZM49W3E) and their resulting hybrids, according to the study objective, from fifteen different inbreed lines with flowering time. The five inbreed lines were planted for four seasons (spring and fall 2019) and (spring and fall 2</p> ... Show More
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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Engineering
Civilizations and Environmental Particulars of Place in Islamic Holy Thresholds in Iraq (Alkadhumain Holy Threshold as a case study)
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Islamic shrines architecture is one of the Islamic Architectural building types. It is called (Thresholds); (Atabat) in Arabic. Thoroughbred throughout the Islamic world from the east to west. In addition, it carries the style features and peculiarities of uniqueness from the rest of the types of Islamic architecture. By virtue of the particularity of its function as tomb for important person in Islamic history. Islamic shrines architecture has grown and evolved in started from the small shrines, and then taken to widen with the evolution of time in line with the value of the event and the rituals associated with it. Some of them to became centers of large cities of the largest in many parts of the Islamic world.

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