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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 Jun 01 2012
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Contribution of Privatization in Tax Revenues: an applied research on a sample of filling stations
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The tax revenues achieved through projects of transition to private sector are regarded as an important source for using in achieving political, economic and social objectives. Since Iraq is heading towards free market economy, new strategies should be adopted to reform the taxation system from by a qualified taxation management office and to activate the taxation policy and to reconsider legislation in relation to the aware of the legible to the importance of disclosure of their taxable real income in order to arrive at contribution of privatization in the taxation revenues for the important role effect on economic activities. In the light of the above, the research is based upon a hypothesis which stipulates that privatization contribu

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Publication Date
Fri Mar 01 2013
Journal Name
International Journal Of Recent Research And Review
Influence of Discharge Pressure on the Plasma Parameter in a Planar Dc-Sputtering Discharge of Argon
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Abstract- Plasma parameters in a planar dc-sputtering discharge in argon were measured by cylindrical electrostatic probe (Langmuir probe).Electron density, electron temperature, floating potential, and space potential were monitored as a function of working discharge pressure. Electrostatic probe and supporting circuit were described and used to plot the current – voltage characteristics. Plasma properties were inferred from the current-voltage characteristics of a single probe positioned at the inter-cathode space. Typical values are in the range of (10-16 -10-17) m-3 and (2.93 – 5.3) eV for the electron density and the electron temperature respectively.

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Publication Date
Tue Jan 01 2019
Journal Name
Aerosol And Air Quality Research
Effect of Inner Rod Tilting on the Performance of a Cylindrical Differential Electrical Mobility Analyzer (DEMC)
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Publication Date
Sun May 24 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Assessment of dental arches symmetry in a sample of Iraqi children at the mixed dentition stage
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Background: Little is known about asymmetry of children's dental arches, the purpose of this study was to verify the presence of asymmetry of dental arches among Iraqi children in the mixed dentition stage. Materials and methods: The sample included 52 pairs of dental casts, 27 pairs belong to males and 25 pairs for females. Three linear distances were utilized on each side on the dental arch: Incisal-canine distance, canine-molar distance and incisal-molar distance, which represent the dental arch segmental measurements using the digital sliding calipers, which is accurate up to 0.02 mm. Results: No significant sides' differences with high correlation coefficient were found between the right and left incisal-canine, canine-molar and in

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Publication Date
Tue Oct 04 2022
Journal Name
Lecture Notes In Mechanical Engineering
Effect of Stator Core Materials on the Performance Characteristics of a Free Piston Linear Generator Engine
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Publication Date
Mon Sep 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Obstacles to the application of total quality management program in a number of iraqi service organizations
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The research aims to statement the main obstacles that prevent the application of total quality management (TQM) in a number of Iraqi service organizations, and by one organization in each of the sectors (health, finance, education, higher education, tourism), which are, (Al-Yarmouk Teaching Hospital, Rafidain Bank/ Branch of Hay Al-Arabi Al-Jadid, Al-Karkh/1 Directorate of Education, College of administration and Economics/ Baghdad University, International Palestine Hotel). The research also, tries to classify the priority of the obstacles depending on the type of service organization surveyed. And diagnoses the extent to which or the difference of the research sample members views on the order of obstacles of TQM, and also proposes a

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Publication Date
Wed Aug 17 2022
Journal Name
Sustainability
Experimental Evaluation of the Thermoelectrical Performance of Photovoltaic-Thermal Systems with a Water-Cooled Heat Sink
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A design for a photovoltaic-thermal (PVT) assembly with a water-cooled heat sink was planned, constructed, and experimentally evaluated in the climatic conditions of the southern region of Iraq during the summertime. The water-cooled heat sink was applied to thermally manage the PV cells, in order to boost the electrical output of the PVT system. A set of temperature sensors was installed to monitor the water intake, exit, and cell temperatures. The climatic parameters including the wind velocity, atmospheric pressure, and solar irradiation were also monitored on a daily basis. The effects of solar irradiation on the average PV temperature, electrical power, and overall electrical-thermal efficiency were investigated. The findings i

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Publication Date
Sun Sep 01 2013
Journal Name
Baghdad Science Journal
Synthesis of some heterocyclic derivatives of 1,8-Naphthyridine with a new substitution on the Naphthyridine ring
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Abstract The Synthesis in good yields of some new 1,8-Naphthyridine derivatives (1-9) and characterized on the basis of IR and 1H NMR spectra data. The compounds (1) and (6) were utilized as a starting material for the preparing of these compounds.

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Publication Date
Thu Jul 01 1999
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
A new species of grape-nune leafhopper of the genus Arboridia Zakhvathin (Homoptera : Cicadellidae) from Iraq
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The present study introduces description of a new species of genus Arboridia Zakhvaticin 1946, based on a large collection of Cicadellids. External morphological characters particularly male genitalia were discussed and illustrated. The genus Arboridia Zalchvatkiia (Typhlocybinae: Erythroneurini) contains small slender, fragil and attractively coloured and patterned leafhoppers. It was erected by Zakhvatkin in 1946 (Zalchvatkin, 1946). The overall length of adults ranges from 2.5 to 3.4 mm. Members of this genus can be recognized by inner apical cell of forewing which is long with oblique base; Cu confluent with this base at a point near the middle of the length of inner apical cell; two prominent circular deep brown spots on vertex (Zal

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Publication Date
Thu Apr 29 2021
Journal Name
International Journal Of Pavement Engineering
An assessment of lime-cement stabilisation on the elastic and resilient moduli of a clayey soil
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