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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 10 2021
Journal Name
Baghdad Science Journal
New Method for the On-Line Determination of Molybdenum Via New Microphotometric Home Mode Instrument, Using Hight Emitting Diode as a Variable Intensity Radiant Source with a Miniture Photosilicone Diode Detector for System: Molybdenum(VI)-Hydrogen Peroxide-Ammonium Solution
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This research work aims to the determination of molybdenum (VI) ion via the formation of peroxy molybdenum compounds which has red-brown colour with absorbance wave length at 455nm for the system of ammonia solution-hydrogen peroxide-molybdenum (VI) using a completely newly developed microphotometer based on the ON-Line measurement. Variation of responses expressed in millivolt. A correlation coefficient of 0.9925 for the range of 2.5-150 ?g.ml-1 with percentage linearity of 98.50%. A detection limit of 0.25 ?g.ml-1 was obtained. All physical and chemical variable were optimized interferences of cation and anion were studied classical method of measurement were done and compared well with newly on-line measurements. Application for the use

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Publication Date
Tue Mar 31 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance of Corrosion Inhibitors Blend for Simulated Industrial Cooling Waters under Dynamic Conditions
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   The inhibitive action of a blend of sodium nitrite/sodium hexametaphosphate (SN+SHMP) on corrosion of carbon steel in simulated cooling water systems (CWS) has been investigated by weight loss and electrochemical polarization technique. The effect of temperature, velocity, and salts concentrations on corrosion of carbon steel were studied in the absence and presence of mixed inhibiting blend. Also the effect of inhibitors blend concentrations (SN+SHMP), temperatures, and rotational velocity, i.e., Reynolds number (Re) on corrosion rate of carbon steel were investigated using Second-order Rotatable Design (Box-Wilson Design) in performing weight loss and corrosion potential approach. Electrochemical polarization measurements

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Publication Date
Sun Jan 02 2022
Journal Name
Journal Of The College Of Languages (jcl)
Ideological Polarization as a Deception Strategy in the Discourse of American Think Tanks: A Critical Discourse Analysis
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Deception is an inseparable facet of political discourse in attaining strategic political gains though compromising public opinion. However, the employment of discursive deception strategies by the policy-making institutions of think tanks has not received due attention in the literature. The current study aims at exploring how the ideologizing deception strategies are utilized by the conservative American think tank of the Washington Institute to reproduce socio-political realities and re-shape public opinion. To fulfill this task, van Dijk’s (2000) notion of ideological polarization which shows positive self-representation and negative other representation is adopted to conduct a critical discourse analysis of four Arabic texts relea

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Publication Date
Mon Jan 02 2017
Journal Name
Journal Of The College Of Languages (jcl)
Magic comparative study of the Old Testament mediator
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Magic is an attempt to affect people or events either by cheating and charlatanry means or by expecting devil powers in order to bring advantage or to avoid a harm or to bring harm to others or to for see the future and divition .

     Magic is either real by the devil like writing majic works to prevent the marriage of someone and to depart the husband and his wife , causing someone to be distressed the physical and nervous diseases and stopping the stories and the project; majic can be artificial by being intellect and legerdemain and different types of triks and to cancel the magic by using magic or by protecting the self by using Talismans as well as presenting or offering sacrificers to the masters and th

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Radiological age estimation using third molars mineralization in a sample attending orthodontic clinics (A retrospective study)
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Background: The evaluation of the chronological age is a practical method in crime investigation field that assists in identifying individuals to treat them as underage or adult. This study aimed to assess the stages of third molars mineralization in relation to chronological age of Iraqi individuals, determine the gender differences and arches (maxillary/mandibular) differences.

Materials and Methods: A total of 300 orthopantomograms of orthodontic patients were collected according to specific criteria and evaluated visually. The developmental stages of maxillary and mandibular third molars were determined according to Demirjian method. T

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Publication Date
Mon Sep 30 2024
Journal Name
Iraqi Journal Of Science
Use of Scalp Hair as a Biomarker to Determine Airborne Heavy Metal Concentrations for the Academic Laboratory Employees
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Academic chemical laboratories (ACL) are considered public places  the employees come in contact with a variety of pollutants. The aim of the current study was to detect heavy metals levels in the indoor air of ACL in two universities in Baghdad city and assess their levels in the academic employees’ scalp hair as biomarkers. Air samples inside ACL were collected to detect Fe, Cd, Zn, Pb and Cu. Scalp hair samples were collected from 40 adult chemical laboratory employees aged 30-60 years, who worked 5 days/week for 6 hours a day. Personal information relating to employees such as age, duration of exposure, smoking habit and sex, was collected as a questionnaire. The results of this study concluded that academic laboratory employ

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Publication Date
Wed Dec 25 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Peaceful settlement as a means of preventing tax: An applied research in the General Commission for Taxation evasion
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The reconciliation of tax reconciliation is one of the legal methods used by the financial authority in Iraq, which is done with the taxpayer

The research dealt with the weakness of tax revenues for many reasons, including tax evasion, which led to the search for ways to reduce evasion to increase the tax revenue, and settlement reconciliation one of these means .

The research proceeded from the premise that the use of a more broadly settled settlement would govern the tax evasion of taxpayers.

The researchers used a series of studies and previous research, books and other sources related to the subject of research, and this was done through the theoretical framework, and the practical aspect that included the fin

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Publication Date
Sun Apr 14 2024
Journal Name
Kufa Journal For Agricultural Sciences
Growth and production of three potato cultivars as affected by organic foliar nutrition
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Publication Date
Mon Aug 03 2020
Journal Name
Rawal Medical Journal
Surgical fixation and grafting of traumatic distal tibia atrophic nonunion with or without platelet-rich plasma: A comparative study
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Objective: To compare distal tibia nonunion plating and grafting with and without platelet-rich plasma (PRP) regarding union rate, union time and complications Conclusion: Combining PRP with autologous bone graft results in a higher union rate, less healing duration, less post-operative pain, and more callus formation. (Rawal Med J 202;45:629- 632). Methodology: In this prospective comparative study, 32 patients with nonunion tibia from July 2017 January 2019 were divided into two groups: group A (16 cases) were treated by plating and grafting with PRP and group B (16 cases) were treated by plating and grafting only. Keywords: Tibial nonunion, bone graft, plateletrich plasma. Results: There was higher union rate in group A related to group

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Publication Date
Mon Jun 08 2020
Journal Name
Research Journal Of Chemistry And Environment
High Performance Liquid Chromatographic and Areaunder Curve spectrophotometric Methods forEstimation of Cefixime in Pure and MarketedFormulation: A Comparative Study
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Cefixime is an antibiotic useful for treating a variety ofmicroorganism infections. In the present work, tworapid, specific, inexpensive and nontoxic methods wereproposed for cefixime determination. Area under curvespectrophotometric and HPLC methods were depictedfor the micro quantification of Cefixime in highly pureand local market formulation. The area under curve(first technique) used in calculation of the cefiximepeak using a UV-visible spectrophotometer.The HPLC (2nd technique) was depended on thepurification of Cefixime by a C18 separating column250mm (length of column) × 4.6 mm (diameter)andusing methanol 50% (organic modifier) and deionizedwater 50% as a mobile phase. The isocratic flow withrate of 1 mL/min was applied, the temper

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