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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 2023
Journal Name
مجلة ميسان للدراسات الأكاديمية
Enhancing Photostability Of Maxillofacial Silicone By The Addition Of Ultraviolet Absorbing Bisoctrizole:, A Review Of Literature
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Publication Date
Sat Jan 01 2022
Journal Name
Revista Electronica De Veterinaria
The Molecular Identification of Pathogenic E. coli Isolated from Raw Cow Milk and Assessment Their Anti-susceptibility to Medical Plants at Al-Najaf city/ Iraq
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Background: Toxin-producing Shiga Escherichia coli has been identified as a new foodborne pathogen that poses a significant health risk to humans. Shiga toxin-producing Escherichia coli can be found in raw cow milk and its derivatives. A small number of Escherichia coli strains that produce shiga toxin are pathogenic. Aim of study: The study aimed to see if there were any virulence genes in 50 milk samples that were typical of Entero-haemorrhagic E. coli and evaluate the Myrtus communis effects on these bacteria. Materials and Method: Milk samples were used to isolate E. coli bacteria (n= 27), biochemically analyzed, and genetically screened for virulence genes using a multiplex (PCR). The hydro-alcoholic extraction of Myrtus communis leave

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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
A Vision to Develop the Effectiveness of the Dissemination of Innovations to Rationalize the Use of Irrigation Water in Iraqi Agriculture
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Abstract<p>Iraqi agriculture faces a major water problem, affecting cultivated areas, agricultural production, farmers’ incomes and food security. However, the results achieved in rationalizing the use of irrigation water are still limited and do not match what they should be in order to meet this serious challenge. The study aimed to provide a vision for the development of the effectiveness of the dissemination of innovations to rationalize the use of irrigation water in Iraqi agriculture. In light of the framework of the dissemination of agricultural innovations, factors related to their effectiveness, and the summary of the Iraqi experience in the field of dissemination of modern irrigation</p> ... Show More
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Publication Date
Thu Jun 01 2017
Journal Name
Journal Of The College Of Languages (jcl)
ההשפעה והשענוע בנאום הפוליטי של שמעון פרס עיון פרגמטי בדוגמאות נבחרות מנאומיו Effect and Persuasion in the Political Discourse of Shimon Peres A Pragmatic Study in Selected form of His Addresses
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במחקר הזה ניתחנו מספר נאומים של שמעון פרס, אנחנו התמקדנו בהשפעה והשכנוע אצל שמעון פרס ואיך הוא יכול להעביר את המסרים של נאומיו בסגנון פרגמטי כדי להגיע ללבו של הציבור.

 גם כן, התמקדנו בסגנון הפוליטי שהוא חושב כי התחום הזה צריך להיות ברור מול הציבור וגם כן מול דעת הקהל הבינלאומי מתוך השימוש במונחים בעלי השפעה ושכנוע להגיע למטרות המבוקשות.

 במלים אחרות, שמעון פרס, לעתים, מתמקד בשפה מליצית ויעמוד הרב

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Publication Date
Sun Jun 20 2010
Journal Name
Al-qadisiya Journal For Science
Synthesis 4-phenyl -1-alkyl-1,2,4-triazoline-5-one derived from D- fructose
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The aim of the present work is the synthesis of new carbohydrate derivatives containing 1,2,4-triazole from D-fructose . To obtain these derivatives, the diacetone fructose (1 ) was chosen as the starting material, which was obtained from the reaction of anhydrous fructose with dry acetone in presence of anhydrous ferric chloride. Oxidation of ( 1) with potassium permanganate in potassium hydroxide solution gave the acid ( 2). Esterification of the acid with dimethyl sulphate gave the methyl ester (3 ). Treatment of the methyl ester (3 ) with hydrazine hydrate gave the hydrazide (4 ), which is the desired Chiron. The hydrazide (4 ) was used for the preparation of 1,2,4-triazole-5-one (6 ) derivative. These compounds was synthesized by the i

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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Project Planning & Scheduling: بحث تطبيقي لمشاريع / مديرية الابنية المدرسية /دائرة المشاريع /مشروعالوزارةرقم (1)
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Construction project life-cycle processes must be managed in a more effective and predictable way to meet project stakeholder needs , However, there is increasing concern about whether know-how effectively improves  understanding of underlying theories of project management processes for construction organizations and their project managers  Project planning and scheduling are considered as key and challenging tools in controlling and monitoring project performance , but many worldwide construction projects appear to give insufficient attention to effective management and definition of  project  planning, including pre planning stages . Indeed, some planning issues indeed, some planning issues have been completely ove

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Publication Date
Thu Jan 31 2019
Journal Name
Journal Of The College Of Education For Women
Comparison Study in Sarcasm For University of Baghdad Staff
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Sarcasm is conceders one patterns of undesirable communication, which causes social problems in humans relationships because of the contradictory verbal and nonverbal expressions is known sarcasm may defined , statements with intent to belittle others in different situations, dealing with the individual deliberately, to diminish the will or overwhelmed by the recipe stupid, which generate a reaction when a person listener, raising the intentions of ridicule and undermine it, and this may happen is different from the irony interest increased in sarcasm since the development of scientists "Watzlawick '" and Bevin "Jackson's" in 1967 theory interactive and considered the sarcasm one interaction patterns in the social relationship, which use

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Physics: Conference Series
Experimental study of some shielding parameters for composite shields
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Publication Date
Sun Jun 01 2014
Journal Name
مجلة كلية مدينة العلم الجامعة
Palynological study for nine cultivated species of Asteraceae family
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The current research included palynological study for nine ornamental cultivated species of Asteraceae family. The study included measurement the dimensions of pollen grains and there shape in polar view and equatorial view, sculpturing,colpi length and width, spines length and number of spines rows between colpiand exine thickness, the study showed variations in pollen grains characters forthe studied taxa

Publication Date
Sat Dec 31 2016
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance Study of Electrodialysis for Treatment Fuel Washing Wastewater
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In this work, electrodialysis (ED) has been demonstrated to be appropriate technique for reducing the electrical conductivity of real wastewater from fuel washing unit, which has been previously treated by other electrochemical technology (electrocoagulation and electrooxidation).  A five cell electrodialysis stack, with an active membrane area of 60 cm2 per cell was employed. During a batch recirculation mode ED system, the effects of parameters such as electrical potential applied (6-18 V) and flow rate of streams (0.5-1.7 L/min.) on the performance of the total dissolved solids (TDS) separation and specific power consumption (SPC) were studied. The results indicate that the process of ED under potential (15 V) and flow

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