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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 Feb 20 2019
Journal Name
Political Sciences Journal
Illegal migration and the European Union " a perusal of securing the phenomenon"
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Abstract This study seeks to deal academically with how the EU treats clandestine immigration, through adopting a purley security approach, based on the European understanding of security threats posed to the security of communities and States in EU at all levels. So they agreed upon criminalizing this threat within the bloc while using repressive tools and steps to limit illegal immigrants flow to European territories. Accordingly, the EU gave the phenomen a security character. So it takes it from low politics level , that of employment and economic field to that of high politics, as a new security problem lying within a new security language embraced by ruling European elites, in other words EU touched on this issue as a speech act emp

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Publication Date
Thu Jan 31 2019
Journal Name
Journal Of The College Of Education For Women
A New Vision in the Locality and the Factors of Forming Meander
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The research addressed an analytical field investigation of the locality of meander, the factors responsible of the locality of the meander at certain points of the stream other than others, and the role sequence of these factors in the formation process.
The research revealed that the location of forming the meander was associated closely with the scale structural composition of the bank materials from which the first stage of forming the curved stream, for the inhomogeneous or non-identical opposite banks in their scale structural composition saw an activity of differential corrosion, while the homogeneous and identical opposite banks in their scale structural composition saw an identical corrosion activity in its intensity at both

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Publication Date
Tue Jan 01 2013
Journal Name
Brain Research Bulletin
A note on the probability distribution function of the surface electromyogram signal
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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The contribution of the tax authorities to increase the tax revenues: An applied research on a sample of the supporting bodies in the health sector for the period 1998-2008
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the research was exposed to a study the importance of the role of the supportive entities in providing the useful information to the tax administration and their ability to extend the level of the tax base of taxpayers, through the improvement of the tax payers determination and their tax settle for the purpose of increasing the tax revenue, and shed light on the legal evidence through which these entities become officially assigned to perform a supplementary task to the General Committee for Taxes GCT, to help it to perform its task efficiently, and to study the reasons of the weak cooperation of the supportive entities and their reluctance to provide useful information which leads to limiting the tax base.

The research data hav

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Publication Date
Sun Jan 01 2023
Journal Name
Physical Mesomechanics Of Condensed Matter: Physical Principles Of Multiscale Structure Formation And The Mechanisms Of Nonlinear Behavior: Meso2022
Calculation of radon gas concentrations in administration rooms for a number of schools in Diyala governorate
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Publication Date
Sun Jan 30 2022
Journal Name
Heat Transfer
Theoretical and experimental investigation of a heat pipe heat exchanger for energy recovery of exhaust air
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Heat pipes and two‐phase thermosyphon systems are passive heat transfer systems that employ a two‐phase cycle of a working fluid within a completely sealed system. Consequently, heat exchangers based on heat pipes have low thermal resistance and high effective thermal conductivity, which can reach up to the order of (105 W/(m K)). In energy recovery systems where the two streams should be unmixed, such as airconditioning systems of biological laboratories and operating rooms in hospitals, heat pipe heat exchangers (HPHEs) are recommended. In this study, an experimental and theoretical study was carried out on the thermal performance of an air‐to‐air HPHE filled with two refrigerants as working fluids, R22 and R407c. The heat pipe he

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Publication Date
Tue Dec 01 2020
Journal Name
International Journal Of Electrical And Computer Engineering (ijece)
A Haptic feedback system based on leap motion controller for prosthetic hand application
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Leap Motion Controller (LMC) is a gesture sensor consists of three infrared light emitters and two infrared stereo cameras as tracking sensors. LMC translates hand movements into graphical data that are used in a variety of applications such as virtual/augmented reality and object movements control. In this work, we intend to control the movements of a prosthetic hand via (LMC) in which fingers are flexed or extended in response to hand movements. This will be carried out by passing in the data from the Leap Motion to a processing unit that processes the raw data by an open-source package (Processing i3) in order to control five servo motors using a micro-controller board. In addition, haptic setup is proposed using force sensors (F

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Publication Date
Sat Oct 18 2025
Journal Name
Pattern Recognition And Artificial Intelligence
Utilizing Energy-Efficient Deep Learning Technique for Age Estimation Through a Hybrid Methodology
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This study employs evolutionary optimization and Artificial Intelligence algorithms to determine an individual’s age using a single-faced image as the basis for the identification process. Additionally, we used the WIKI dataset, widely considered the most comprehensive collection of facial images to date, including descriptions of age and gender attributes. However, estimating age from facial images is a recent topic of study, even though much research has been undertaken on establishing chronological age from facial photographs. Retrained artificial neural networks are used for classification after applying reprocessing and optimization techniques to achieve this goal. It is possible that the difficulty of determining age could be reduce

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Publication Date
Tue Oct 01 2019
Journal Name
Biochemical & Cellular Archives
A RE-SATURATION IMPACT ON SOIL RETENTION CURVE FOR FIVE DIFFERENT TEXTURED SOILS
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Soil water retention curves (SWRCs) are crucial for characterizing soil moisture dynamics and are particularly relevant in the context of irrigation management. A study was carried out to obtain the SWRC, inflection point, S index, pore size distribution curve, macro porosity, and air capacity from samples submitted to saturation and re-saturation processes. Five different-texture disturbed soil samples Sandy Loam, Loam, Sandy Clay Loam, Silt Loam, and Clay were collected. After obtaining SWRC, each air-dried soil samples were submitted to particle size distribution and clay dispersed in water analyses to verify the soil lost clay. The experimental design was completely randomized with three replications using two processes of SWRC (saturat

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Publication Date
Tue Jan 01 2019
Journal Name
Energy Procedia
Quadrupole Moment & Deformation Parameter for Even-Even 38Sr (A=76-102) Nuclide
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