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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
Tue Sep 01 2020
Journal Name
Baghdad Science Journal
In Silico Characterization of a Cyclin Dependent Kinase -A (CDKA) and its Coding Gene in some Oryza Species
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Rice (Oryza sativa) is a fundamental food for the majority of world population. Cyclin Dependent Kinase -A (CDKA) accelerates transition through different stages of cell cycle and contributes in gametes formation. In the present investigation, a CDKA encoding gene along with the corresponding protein were characterized in O. sativa Indica Group, O. glaberrimaO. barthii, O. brachyantha, O. glumipatula, O. longistaminata, O. meridionalis, O. nivara, O. punctata and O. rufipogon using in silico analyses. The results reflected little variation in most species except O. longistaminata and O. brachyantha. Compared with the remaining species, O. longistaminata

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Publication Date
Sun Jun 03 2012
Journal Name
Al-kindy College Medical Journal
Ultrasound of the Rotator Cuff: A Comparison of Ultrasonographic and Physical Examination Finding in SeventyCases
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Background : Shoulder pain is a common problem that can pose difficult diagnostic and therapeutic challenges for the family physician It is the third most common musculoskeletal complaint in the general population, and account for 5% of all general practitioners musculoskeletal consults Objective: To determine the diagnostic performance of ultrasonography compared with the physical examination for detection of rotator cuff tears in painful shoulder syndrome. Method: Prospective study was done on seventy patients (48 male, 22 female), age ranged between 30-70 years (mean age 50 years), From February 2007 to July 2011, were subjected to comparative study in Al-Kindy teaching hospital with rotator cuff tears, including physical and ultrasonogr

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Publication Date
Sun Dec 30 2007
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Feed Concentration on the Production of Pregelatinized Starch in a Double Drum Dryer
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Double drum dryer is operated for producing pregelatinized maize starches using feed starch slurries of different
solids(7, 10 and13 g/100 g )content . Steam pressure (2,3,and 4 bar), the level of pool between the drums (4,7,and 10
cm) , and speed of drums rotation (3,4,and 6 rpm) are varied together with the feed solids content in a practical range of
values. The response of the dryer is registered by measuring several output variables, i.e. external drum temperature,
product moisture content, mass flow rate.

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Publication Date
Tue Aug 01 2023
Journal Name
Journal Of Engineering
The Role of Project Health Check Reports in Identifying Indicative Factors of a Troubled Project
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Government-sponsored projects in Iraq significantly improve the economic situation and provide services but face high rates of troubling blocks. This work aims to identify indicative factors of the Troubled Project using periodic health check reports based on a literature review and interviews with Iraqi experts. As a result, a questionnaire was prepared that included four sections. The first is personal information; the second section is information about knowing the level of institutions’ implementation of project management through prepared documents. The third section is about indicative factors for the project's trouble, including 25 workers; the fourth section is about the questions in the periodic reports to che

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Publication Date
Mon Jan 01 2024
Journal Name
2nd International Conference For Engineering Sciences And Information Technology (esit 2022): Esit2022 Conference Proceedings
Ideals of the full transformation semigroup of a free left G-act on n-generators
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Publication Date
Wed May 02 2018
Journal Name
Chempluschem
The Oxidation of Peroxide by Disordered Metal Oxides: A Measurement of Thermodynamic Stability “By Proxy”
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It is often noted that disordered materials have different chemical properties to their more “ordered” cousins. Quantifying these effects in terms of thermodynamics is challenging in part because disordered materials can be difficult to characterize and are frequently relatively unstable. During the course of our experiments to understand the effects of disorder in catalysts for water oxidation we observed that many disordered manganese and cobalt oxide water oxidation catalysts directly oxidized peroxide in contrast to their more ordered analogues which catalyzed its disproportionation, that is, MnO2+2H+ +H2O2! Mn2+ +2H2O+O2(oxidation) versus H2O2!H2O+1=2 O2(disproportionation). By measuring the efficiency for one reaction over the oth

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Publication Date
Mon Jan 01 2024
Journal Name
Aims Energy
The impact of different compression ratios on emissions, and combustion characteristics of a biodiesel engine
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<p>The current work investigated the combustion efficiency of biodiesel engines under diverse ratios of compression (15.5, 16.5, 17.5, and 18.5) and different biodiesel fuels produced from apricot oil, papaya oil, sunflower oil, and tomato seed oil. The combustion process of the biodiesel fuel inside the engine was simulated utilizing ANSYS Fluent v16 (CFD). On AV1 diesel engines (Kirloskar), numerical simulations were conducted at 1500 rpm. The outcomes of the simulation demonstrated that increasing the compression ratio (CR) led to increased peak temperature and pressures in the combustion chamber, as well as elevated levels of CO<sub>2</sub> and NO mass fractions and decreased CO emission values un

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Publication Date
Wed May 14 2025
Journal Name
Journal Of Applied Mathematics
Role of Wind and Fear on the Dynamic of a Prey and Two Competing Predators
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An essential tool for studying the web is its ability to show how energy moves through an ecosystem. Understanding and elucidating the relationship between species variety and their placement within the inclusive trophic dynamics is also beneficial. A food web ecological model with prey and two rival predators under fear and wind flow conditions is developed in this article. The boundedness and positivity of the system’s solution are established mathematically. The stability and existence constraints of the system’s equilibria are examined. The proposed system’s persistence limitations are established. Additionally, the bifurcation analysis of every potential equilibrium is examined using the Sotomayor theorem. To describe the

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Publication Date
Tue Jan 18 2022
Journal Name
Heat Transfer
Effect of receiver geometry on the optical and thermal performance of a parabolic trough collector
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Abstract<p>In this study, the optical and thermal performance of a Parabolic Trough Collector PTC system is investigated theoretically. A series of numerical simulations and theoretical analysis has been conducted to investigate the effect of the receiver geometry and location relative to the focal line on its optical performance. The examined receiver geometries are circular, square, triangular, elliptical and a new design of circular‐ square named as channel receiver. The thermal performance of PTC is studied for different flow rates from (0.27 to 0.6 lpm) theoretically. Results showed that the best optical design is the channel receiver with an optical efficiency of 84% while the worst is the elliptical </p> ... Show More
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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of accounting disclosure in granting bank financing A field study ona sample of banks operating in the state of Gezira 2022 AD: (دراسة ميدانية على عينة من المصارف العاملة في ولاية الجزيرة 2022م)
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                 The aim of the research is to identify the adequacy of accounting disclosure in granting bank financing in explaining the role of accounting disclosure in granting bank financing by linking the concepts of full, comprehensive and adequate disclosure to bank financing. The impact of full accounting disclosure on granting bank financing, the existence of an impact of comprehensive accounting disclosure on granting bank financing, the existence of an impact of adequate accounting disclosure on granting bank financing, and the research relied on the descriptive approach, the deductive and inductive approach, the inferential analytical approach, a

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