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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
Sun Jan 01 2017
Journal Name
Journal Of The College Of Languages (jcl)
השואה והשלכותיה על אהרון אפלפלד - עיון בשלושה סיפורים קצרים עוזר למורה – עלי מוחמד רשיד The Holocaust and its impact on Aharon Bielefeld - A Study in Three Short Stories
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מטרת המחקר הזה היא לבדוק את שלושה סיפורים קצרים מהקובץ הראשון של אהרון אפלפלד , שנחשב ההצהרה הרשמית על היותו סופר השואה הראשון בישראל , המשותף לשלושת הסיפורים הוא הנימה של הגיבורים היוצאים למסע פיזי ונפשי לגלות את אשר אירע להם , מגמתו של המחקר היא לבדוק את הצורה המיוחדת שבה אפיין אפלפלד את גיבוריו שמעידים על כך , כי השואה היא החוויה המרה והקשה בקרב היהודים והשלכותיה נשארה טמונה בקרבם גם אחרי המלחמה ואחרי שנים

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Publication Date
Tue Jan 01 2019
Journal Name
Acta Facultatis Medicae Naissensis
Operative treatment of femoral neck fractures with cannulated screws with and without platelet rich plasma in young adults: A comparative study
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Many studies have evaluated the effect of platelet rich plasma (PRP) in the treatment of non-union fractures but few studies have investigated their effect on the union of femoral neck fractures or their functional outcome in young adults. The aim of this study was to evaluate the union time and functional outcome in young adult patients with femoral neck fracture managed by three cannulated screws injected with PRP and those managed by fixation only. This prospective study included 24 patients diagnosed with femoral neck fractures within 24 hours of presentation. Twelve cases in group A were managed by closed reduction and three cannulated screws fixation injected with PRP; twelve patients in group B were managed only by closed reduction a

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Publication Date
Tue Dec 11 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Evaluation of Nursing staff Performance in Cardiac Care Units at Teaching and Non Teaching Hospitals in Kirkuk City: A Comparative Study
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Objective: The descriptive study was used to evaluate nursing staff performance in cardiac care units at teaching
and non teaching hospitals in kirkuk city: A comparative study.
Methodology: A descriptive study was used to evaluate nursing staff performance in cardiac care units. The study
was conducted from December 29th
, 2013 up to the 27th of Apr. 2014. A non-probability (purposive) sample of
(44) nurses who work in cardiac care unit at Azady teaching Hospital and Kirkuk general Hospital was evaluated by
a questionnaire which consisted of two parts; the first part is concerned with the demographic characteristics of
the nurses and the second part concerned Observation check list for evaluation nursing staff Perfo

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Publication Date
Wed Aug 20 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Fracture resistance of weakened premolars restored with sonically-activated composite, bulk-filled and incrementally-filled composites(A comparative in vitro study)
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Background: This study was conducted to assess the effect of sonic activation and bulk placement of resin composite in comparison to horizontal incremental placement on the fracture resistance of weakened premolar teeth. Materials and method: Sixty sound human single-rooted maxillary premolars extracted for orthodontic purposes were used in this study. Teeth were divided into six groups of ten teeth each: Group 1 (sound unprepared teeth as a control group), Group 2 (teeth prepared with MOD cavity and left unrestored), Group 3 (restored with SonicFill™ composite), Group 4 (restored with Quixfil™ composite), Group 5 (restored with Tertic EvoCeram® Bulk Fill composite) and Group 6 (restored with Universal Tetric EvoCeram® co

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Publication Date
Sat Jun 18 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Anti-Inflammatory Activity of Gingko Biloba Extract in Cotton Pellet-Induced Granuloma in Rats: A comparative Study with Prednisolone and Dexamethasone
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The current study was designed to evaluate the anti-inflammatory effect of GKB in the rat model of granulomatous inflammation. Thirty rats were distributed into five groups:  The first group served as negative control group that received distilled water (DW) only without inducting inflammation, positive control group; treated with DW with the induction of inflammation and they were assigned to cotton pellet-induced granuloma, ginkgo biloba (GKB) treated group (200mg/kg/day), dexamethasone-treated group (1mg/kg), and Prednisolone treated group (5mg/kg). All the treatments were given orally for seven consecutive days.  On day eight, the rats were anesthetized and the pellets together with granulation tissue were carefully removed

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Publication Date
Wed Aug 20 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A Comparative Study of Clinicopathological and Immunohistochemical Expression of CD1a, RANK and RANKL in Langerhans Cell Histiocytosis of Jaw and Skull Lesions
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Background: Langerhans' cell histiocytosis (LCH) is a group of conditions affecting the reticuloendothelial system. It includes Letterer-Siwe disease, Hand-Schuller-Christian disease and eosinophilic granuloma and most often presents in childhood. Materials and methods: Twenty-five cases of LCH were diagnosed histologically and confirmed by CD1a antibody and assessed immunohistochemically using anti-RANKL and anti-RANK antibodies to evaluate osteoclastogenic mechanism. Results: Regarding jaw cases, there was a significant correlation between CD1a and RANK (P=0.016). While in the skull, highly significant correlation existed between RANK and RANKL (p=0.001). Among the sites, there was no statistically significant difference found for each

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Publication Date
Wed Jun 28 2023
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
PREPARATION OF A COMBINATION OF NANO- MEDICINAL PLANTS AS ANTIOXIDANTS AND MICROORGANISMS: PREPARATION OF A COMBINATION OF NANO- MEDICINAL PLANTS AS ANTIOXIDANTS AND MICROORGANISMS
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ABSTRACT

            The controversy is currently revolving around industrial additives, including antioxidants, their negative effects on consumer health and the emergence of various and various diseases, which led scientists and researchers to intensify most studies on natural antioxidants and their synthesis from medicinal plants mentioned in ancient medicine and in divine books as potential antioxidants of increasing importance. Therefore, this study was designed to synthesize silver nitrate particles from plant leaf extracts (Figs, Olives, and Moringa) and study their effect on bacterial inhibition of each of the undesirable Coliform bacteria (E-Coli,

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Publication Date
Mon Aug 17 2020
Journal Name
Biochemical And Cellular Archives
SERUM FERRITIN AS A BIOMARKER FOR THYROID GLAND (HYPO AND HYPER) THYRODISM WITH METABOLIC SYNDROME
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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Serum ceruloplasmin ,copper and iron levels as a risk factors for coronary heart diseases(CHD)
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Ceruloplasmin (Cp) is one of the acute phase protein, in this review ,we studied the level of ceruloplasmin with copper (Cu) and iron in 90 patients with coronary heart diseas ( those patients are divided into three groups, whom are stable angina , unstable angina and myocardial infarction compared with 30 healthy volunteers) and the roles of them as diagnostic and prognostic tools.The diagnosis was attend by a clinical examination carried out by the consult medical staff in Ibn AL-Nafis hospital. The result: ceruloplasmin recorded a significantly(p<0.05)higher level in all patient groups compared with the control, so this result supports the hypothesis that a high serum ceruloplasmin level is a risk factor for coronary heart di

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Publication Date
Fri Jun 01 2007
Journal Name
Journal Of The College Of Languages (jcl)
Old Age as a Motif In the Poetry of W.B. Yeats (1865-1939)
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In 1908 , the American poet Ezra Pound (1885-1972) , the central figure in the modern movement who was the driving force behind several movements , notably Imagism and Vorticism , met the Irish poet W. B. Yeats in London . Pound was employed as his secretary and the two soon became close friends . He found Yeats a realist, symbolist and a metaphysical poet with an uncanny power over words and regarded him the greatest living poet .The poetical style and the occult beliefs of the Irish poet drew the attention of the American Imagist .During the war, Pound and Yeats lived together at Stone Cottage in Sussex studying Japanese literature .Speaking of Yeats , T. S. Eliot described him as "one of those few whose history is the history of their

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