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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
Fri Jan 01 2021
Journal Name
Water Pollution And Management Practices
Existence of Antibiotics in Wastewater as a Pollution Indicator
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Publication Date
Tue Dec 01 2009
Journal Name
Iraqi Journal Of Physics
Spectrophotometrically Analysis of PMMA as a low – Doses Dosimeter
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Polymethylmethacrylate film (PMMA) of thickness 75 μm was evaluated Spectrophotometrically for using it as a low-doses gamma radiation dosimeter. The doses were examined in the range 0.1 mrad-10 krad. Within an absorption band of 200-400 nm, the irradiated films showed an increase in the absorption intensity with increasing the absorbed doses. Calibration curves for the changes in the absorption differences were obtained at 218, 301, and 343 nm. At 218 nm the response for the absorbed doses is a linear in the range 10 mrad- 10 krad. Hence it is recommended to be adopted as an environmental low doses dosimeter

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Publication Date
Fri Aug 09 2024
Journal Name
Theory And Practice In Language Studies
Fallacy as a Strategy of Argumentation in Political Debates
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This study aims to study argumentation in political debates by figuring out the logical fallacies employed in the debates of Clinton and Trump, the presidential nominees of the 2016 elections, and Biden and Trump, the leading contenders in the 2020 United States presidential election. The study attempts to answer the questions: (1) What relevance fallacies are adopted in the debate between Trump and Clinton? (2) What rhetorical devices are used to influence the audience and gain voters besides fallacies in the debates selected? The study analyses two texts from two arguments using Damer's (2009) taxonomy of relevance fallacy and rhetorical devices based on Perrine’s (1969) model of communication and interpersonal rhetoric to answe

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Publication Date
Tue Feb 26 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Role of External Oversight in The Organization of Policy Import: A model of Supreme Audit
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  The construction of development is required to develop various economic sectors with the necessity to meet the various requirement of both individuals and institutions , or through the import process , which must be commensurate with the needs of the market and the economy and development. But in fact , we found that the process of import in Iraq after 2003 took a turn dangerous excesses on limits of philosophy and objectives of the import , which  reflected  the level of national production as well as the policy of dumping and given to the lack of matching a lot of goods and materials imported for Standards and Measures of quality and stands behind it causes many of them exposure to the market and weak sectors with an o

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Role of External Oversight in The Organization of Policy Import: A model of Supreme Audit
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The construction of development is required to develop various economic sectors with the necessity to meet the various requirement of both individuals and institutions , or through the import process , which must be commensurate with the needs of the market and the economy and development. But in fact , we find that the process of import in Iraq after 2003 took a turn dangerous excesses on limits of philosophy and objectives of the import , which is reflected at the level of national production as well as the policy of dumping and given and the lack of matching a lot of goods and materials imported for Standards and Measures of quality and stands behind it causes many of them exposure to the market and weak sectors with an overlap betwee

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Publication Date
Mon Mar 01 2021
Journal Name
Iraqi Journal Of Physics
Study of the Nuclear Structure of some Neutron Rich Si Isotopes Using Shell Model with Skyrme Interaction
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  Abstract

      The nuclear structure of 28-40Si isotopes toward neutron dripline has been investigated in framework of shell model with Skyrme-Hrtree-Fock method using certain Skyrme parameterizations. Moreover, investigations of static properties such as nuclear densities for proton, neutron, mass, and, charge densities with their corresponding rms radii, neutron skin thicknesses, binding energies, separation energies, shell gap, and pairing gap have been performed using the most recent Skyrme parameterization. The calculated results have been compared with available experimental data to identify which of these parameterizations introduced equivalent results with the ex

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Publication Date
Sat Jun 25 2022
Journal Name
International Journal Of Drug Delivery Technology
Microneedles as A Magical Technology to facilitate Transdermal Drug Delivery: A Review Article
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Skin drug administration is the method used to provide drugs for local or systemic therapy, which is recognized for clinical usage. It is the third-largest method of medication delivery, after only intravenous administration and oral administration. Using a transdermal delivery method makes the administration easy, and blood concentration and adverse effects can be reduced. A microneedle is a micron-sized needle with a short height of no more than 500 micrometers and a width of no more than 50 micrometers. The needle comes into contact with the epidermal layer of the skin before it gets to the dermal layer, where there is no discomfort. Several materials, such as metals, inorganic, and polymer materials, are used to create microneed

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Publication Date
Mon Apr 20 2020
Journal Name
International Medical Journal
Cleaning efficacy and instrumentation time using rotary file system in primary molars (comparative study)
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ABSTRACT— In primary teeth, root canal treatment is a time consuming and challenging procedure, particularly during the most important step in endodontic treatment which is the preparation of the canal. Pulpectomy is the treatment of choice in all the necrotic primary teeth. For better treatment protocol, advancing technology brought the rotary system to reduce the manual dexterity and improve the quality of treatment for pulpectomy. This study aimed to compare and assess the efficacy of cleaning and the time required for the instrumentation during the preparation of root canals of the primary molars using the rotary and the manual (conventional) systems. Thirty root canals of primary teeth were selected. These teeth submitted to a

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Publication Date
Sun Sep 25 2022
Journal Name
Research Journal Of Chemistry And Environment
Synthesis, Antioxidant ability and Docking study for new 4,4'-((2-(Aryl)-1H-benzo[d]imidazole-1,3(2H)-diyl)bis(methylene))diphenol)
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New series of 4,4'-((2-(Aryl)-1H-benzo[d]imidazole-1,3(2H)-diyl)bis(methylene))Diphenol(3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hydr

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Publication Date
Mon Oct 10 2022
Journal Name
Research Journal Of Chemistry And Environment
Synthesis, Antioxidant ability and Docking study for new 4,4'-((2-(Aryl)-1H-benzo[d]imidazole-1,3(2H)- diyl)bis(methylene))diphenol)
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New series of 4,4'-((2-(Aryl)-1H-benzo[d]imidazole1,3(2H)-diyl)bis(methylene))Diphenol(3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hydroxyl for t

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