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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
Sat Aug 21 2021
Journal Name
Engineering, Technology & Applied Science Research
The Response of a Highly Skewed Steel I-Girder Bridge with Different Cross-Frame Connections
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Braces in straight bridge systems improve the lateral-torsional buckling resistance of the girders by reducing the unbraced length, while in horizontally curved and skew bridges, the braces are primary structural elements for controlling deformations by engaging adjacent girders to act as a system to resist the potentially large forces and torques caused by the curved or skewed geometry of the bridge. The cross-frames are usually designed as torsional braces, which increase the overall strength and stiffness of the individual girders by creating a girder system that translates and rotates as a unit along the bracing lines. However, when they transmit the truck’s live load forces, they can produce fatigue cracks at their connection

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Publication Date
Sun Jan 01 2023
Journal Name
Technologies And Materials For Renewable Energy, Environment And Sustainability: Tmrees22fr
A theoretical enhancement of electronic transfer dynamics in the D35CPDT dye donor to 𝑻𝒊𝑶𝟐 acceptor
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Publication Date
Sat Feb 01 2025
Journal Name
مجلة واسط للعلوم الانسانية
A Pragmatic Analysis of Emotional Blackmail in the American Movie No One Would Tell (2018)
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Emotional blackmail is generally defined as manipulating others' emotions for personal gain. It is a type of manipulation that damages healthy relationships among people and turns them into toxic relations leaving the victim in a state of depression and under stress of losing something s/he holds dear. This study aims to identify the pragmatic techniques of emotional blackmail used by both blackmailers and victims in "No One Would Tell" (2018).  To do so, the researchers developed an eclectic model comprising Forward and Frazier's (1997) emotional blackmail, Searle’s speech acts (1979), Brown and Levinson’s politeness strategies (1987), Culpeper’s impoliteness strategies (1996, 2005), and Mayfield's taxonomy of fallacy (2007)

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Publication Date
Wed Nov 01 2023
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
The Impact of Implementing a Pharmacist-led Deprescribing Program on Medication Adherence among Hemodialysis Patients
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Background: One way to target polypharmacy and inappropriate medication in hemodialysis (HD) patients is with medication deprescribing. Objective: To assess the impact of implementing a pharmacist-led deprescribing program on medication adherence among HD patients. Method: A prospective interventional, one-group pretest-posttest-only design study was conducted at a hemodialysis center in Wasit Governorate, Iraq. Medication reconciliation followed by medication review based on the deprescribing program was done for all eligible patients, and the patients were monitored for three months for any possible complications. Results: Two hundred and seventy patients were screened for eligibility. Only one hundred and eighteen were enrolled i

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Publication Date
Fri Jan 01 2021
Journal Name
Desalination And Water Treatment
Electrosorption of cadmium ions from the aqueous solution by a MnO2/carbon fiber composite electrode
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The nanostructured MnO2 /carbon fiber (CF) composite electrode was prepared using the anodic electrodeposition process. The crystal structure and morphology of MnO2 particles were determined with X-ray diffraction and field-emission scanning electron microscopy. The electrosorptive properties of the prepared electrode were investigated in the removal of cadmium ions from aqueous solution, and the effect of pH, cell voltage, and ionic strength was optimized and modeled using the response surface methodology combined with Box–Behnken design. The results confirm that the optimum conditions to remove Cd(II) ions were: pH of 6.03, a voltage of 2.77 V, and NaCl concentration of 3 g/L. The experimental results showed a good fit for the Freundli

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Publication Date
Sat Dec 01 2012
Journal Name
Journal Of Engineering
Effect of Oscillatory Motion in Enhancing the Natural Convection Heat Transfer from a Vertical Channel
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This paper reports an experimental study regarding the influence of vertical oscillations on the natural convection heat transfer from a vertical channel. An experimental set-up was constructed and calibrated; the vertical channel was tested in atmosphere at 25o
C. The channel-to-ambient temperature difference was varied with the power supply to the electrical heater ranging between
15W to 70W divided into five levels. Data sets were measured under different operating condition from a test rig under six vibrating velocities (VVs) levels ranging from (5-30 m/s) in addition to the stationary state. The results show that the maximum heat transfer enhancement factor (E) occurs at Rayleigh number (Ra=2.328×103 ) and vibrational Reynol

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Publication Date
Fri Oct 24 2014
Journal Name
Journal Of Religion And Health
Cross-Cultural Validation and Psychometric Properties of the Arabic Brief Religious Coping Scale (A-BRCS)
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Publication Date
Sat Jan 01 2022
Journal Name
International Journal Of Low-carbon Technologies
Performance evaluation of the photovoltaic thermal system with a fin array and surface zigzag layout
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Abstract<p>Solar photovoltaic (PV) has many environmental benefits and it is considered to be a practical alternative to traditional energy generation. The electrical conversion efficiency of such systems is inherently limited due to the relatively high thermal resistance of the PV components. An approach for intensifying electrical and thermal production of air-type photovoltaic thermal (PVT) systems via applying a combination of fins and surface zigzags was proposed in this paper. This research study aims to apply three performance enhancers: case B, including internal fins; case C, back surface zigzags; and case D, combinations of fins and surface zigzags; whereas the baseline smooth duct rep</p> ... Show More
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Publication Date
Wed Feb 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Using Fuzzy Games Theory to Determine the optimal Strategy for The Mobile Phone Networks in The Baghdad And Basra governorates
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      The objective of this research is employ the special cases of  function  trapezoid in the composition of fuzzy sets to make decision within the framework of the theory of games traditional to determine the best strategy for the mobile phone networks in the province of  Baghdad and Basra, has been the adoption of different periods of the  functions belonging to see the change happening in the matrix matches and the impact  that the strategies  and decision-making  available to each player and the impact on  societ

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Publication Date
Fri Jan 01 2021
Journal Name
International Journal Of Agricultural And Statistical Sciences
USE OF MODIFIED MAXIMUM LIKELIHOOD METHOD TO ESTIMATE PARAMETERS OF THE MULTIPLE LINEAR REGRESSION MODEL
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