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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
Mon Jul 01 2019
Journal Name
Journal Of Educational And Psychological Researches
Teaching skills for Public and Private Schools’ Teachers: comparative study : Teaching skills for Public and Private Schools’ Teachers: comparative study
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Abstract:

The great expansion of teaching skills requires finding ways and methods to help teachers acquire experiences of all kinds. The researcher found in the subject of the teaching skills for teachers in public and private schools a fertile field for conducting a study that enables the measurement of these skills. Thus, the study aims to identify the skills of teaching lessons for teachers, the difference in teaching lesson skills for teachers according to the years of service, the differences in teaching lesson skills for teachers according to the specialized teachers and non-specialized teachers, the differences in teaching lesson skills for teachers according to the public and private school. The

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Publication Date
Mon Jan 01 2018
Journal Name
World Journal Of Dentistry
Obturation of Lateral Canals by a New Reciprocating Spreader and a Conventional Finger Spreader by Lateral Condensation Technique: in vitro Comparative Study
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Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Semiotics of Musical Sign in Iraqi Pantomime Show (Ahriman) as a Model: علي عدي صاحب-شيماء حسين طاهر
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The musical sign was associated with the first appearances of acting that are based on human gestures and expressive and silent movements, and they contributed in accentuating and clarifying these gestures and explain their meanings and indications, and they remained with them until these gestures turned into artistic theatrical shows so that the musical sign would have many functions and constitute the main pillars for this kind of show.
The musical sign is a language not much different than the human language in the semiotic analysis. There has been an increased interest in it and its use in the mime shows by the graduates who realized its necessity and significance in the pantomime show intellectually, artistically and aesthetical

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Extent of the Practice of Iraqi Banks to Manage Profits Using the (LLp it) Model and Its Reflection on the Tax Base, A Case Study of A Sample of Iraqi Private Banks Listed in The Iraqi Stock Exchange
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The research aims to identify the extent to which Iraqi private banks practice profit management motivated by reducing the taxable base by increasing the provision for loan losses by relying on the LLP it model, which consists of a main independent variable (net profit before tax) and independent sub-variables (bank size, total debts to total equity, loans granted to total obligations) under the name of the variables governing the banking business. (Colmgrove-Smirnov) was used to test the normal distribution of data for all banks during the period 2017-2020, and then find the correlation between the main independent variable sub and the dependent variable by means of the correlation coefficient person, and then using the multiple

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
A Comparative Study of Heavy Metals and Trace Elements Concentration in Milk Samples Consumed in Iraq
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The measurements of major and trace elements in different brands of milk powder selected from the Iraqis market via the X-ray fluorescence (XRF) Technique have been studied in the present work. The result of the measurements reveals the high concentrations of sodium, phosphorus, sulfur, chlorine, potassium, calcium and magnesium. Furthermore, low concentrations of aluminum, silicon, iron, bromine, molybdenum, iodine, barium, titanium, manganese, cobalt, chrome, nickel, copper, zinc and lead were detected. Neutron activation analysis (NAA) and Kjeldahl technique were also employed to determine the concentrations of nitrogen. It was found that the nitrogen concentration was in the range of (1.96 - 3.23) % which is within the permissible li

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Publication Date
Thu Mar 25 2021
Journal Name
International Journal Of Drug Delivery Technology
A comparative study of retinol-binding protein-4 and progranulin in iraqi women with thyroid disorder
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Thyroid hormones (TH) regulate the metabolic processes required for normal development and growth; also, to organizemetabolism in adults, any defect in thyroid function leads to abnormality in thyroid hormones level. The current study hasbeen designed to find the relationship between retinol-binding protein-4 and progranulin in the serum of Iraqi women withhypothyroidism and hyperthyroidism, also, to study whether these patients are exposed to a risk of developing diabetes mellitus,and PGRN may be a biomarker in detection early stage of diabetes mellitus.Materials and Methods: in this study, serum samples were obtained from 50 Iraqis women patients, [25 patients withhypothyroidism (G2) and 25 patients with hyperthyroidism (G3)] in addition

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Publication Date
Mon Oct 28 2019
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Kinetic profile of silver and zinc oxide nanoparticles by intraperitoneal injection in mice , a comparative study
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Publication Date
Tue Oct 09 2018
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
A COMPARATIVE HISTOLOGICAL STUDY OF THYROID TISSUE IN CARP FISH CYPRINUS CARPSIO AND MICE SWISS ALBICANS
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    This histological study was carried out to compare between the thyroid gland of mice (as a model of the mammals) and the thyroid tissue of fish.  Unlike mice, the thyroid gland of fish can't be recognized by naked eye.  The present study revealed that the thyroid of mice varied from that of fish by the location and the histological structure. The study classified the physiological state of the thyroid of mice into three states and that of the fish into only two states. Accordingly, the study concluded that the metabolism of thyroid fish was of moderate type.

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Publication Date
Sun Dec 09 2018
Journal Name
Baghdad Science Journal
A Comparative Efficiency Study of Two Adsorbent Materials to Remove Eosin Y Dye from Aqueous Solutions
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This study was done to find a cheap, available and ecofriendly materials that can remove eosin y dye from aqueous solutions by adsorption in this study, two adsorbent materials were used, the shells of fresh water clam (Cabicula fluminea) and walnut shells. To make a comparison between the two adsorbents, five experiments were conducted. First, the effects of the contact time, here the nut shell removed the dye quickly, while the C. flumina need more contact time to remove the dye. Second, the effects of adsorbent weight were examined. The nut shell was very promising and for all used adsorbent weight, the R% ranged from 94.87 to 99.29. However C. fluminea was less effective in removing the dye with R% ranged from 47.59 to 55.39. The thi

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
Grammatical Behaviour and Uses of Negative and Prohibitive Particles in Semitic Languages: A Comparative Semitic Study
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      Grammatical particles are so important in understanding a text and its meaning in linguistic context. This paper  " Grammatical Behavior and Uses of Negative and Prohibitive Particles in Semitic Languages: A Comparative Semitic Study"

      tackles  a very important topic in Semitic languages. Comparative studies in Semitic languages shed light on  phenomena in different languages that are related or have one common origin. No doubt, such studies have their own effects on language study in general especially when studying a specific phenomenon and explaining it by reliance on the one origin, or by investigating the various phases of its historical development.

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