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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 Oct 01 2022
Journal Name
Journal Of Engineering
Production Load–bearing Concrete Masonry Units by Using Recycled Waste Crushed Clay Bricks; A Review
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There are serious environmental problems in all countries of the world, due to the waste material such as crushed clay bricks (CCB) and in huge quantities resulting from the demolition of buildings. In order to reduce the effects of this problem as well as to preserve natural resources, it is possible to work on recycling (CCB) and to use it in the manufacture of environmentally friendly loaded building units by replacing percentages in coarse aggregate by volume. It can be used as a powder and replacing of percentages in cement by weight and study the effect on the physical and mechanical properties of the concrete and the masonry unit. Evaluation of its performance through workability, dry density, compressive strength, thermal conduct

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Publication Date
Thu Oct 01 2020
Journal Name
Chemical Engineering And Processing - Process Intensification
Cobalt Removal from Simulated Wastewaters Using a Novel Flow-by Fixed Bed Bio-electrochemical Reactor
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Publication Date
Sat Dec 01 2018
Journal Name
Sustainable Materials And Technologies
A sustainable pavement concrete using warm mix asphalt and hydrated lime treated recycled concrete aggregates
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Recently, increasing material prices coupled with more acute environmental awareness and the implementation of regulation has driven a strong movement toward the adoption of sustainable construction technology. In the pavement industry, using low temperature asphalt mixes and recycled concrete aggregate are viewed as effective engineering solutions to address the challenges posed by climate change and sustainable development. However, to date, no research has investigated these two factors simultaneously for pavement material. This paper reports on initial work which attempts to address this shortcoming. At first, a novel treatment method is used to improve the quality of recycled concrete coarse aggregates. Thereafter, the treated recycled

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Publication Date
Thu Jul 31 2025
Journal Name
Computers, Materials & Continua
A Secure Audio Encryption Method Using Tent-Controlled Permutation and Logistic Map-Based Key Generation
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The exponential growth of audio data shared over the internet and communication channels has raised significant concerns about the security and privacy of transmitted information. Due to high processing requirements, traditional encryption algorithms demand considerable computational effort for real-time audio encryption. To address these challenges, this paper presents a permutation for secure audio encryption using a combination of Tent and 1D logistic maps. The audio data is first shuffled using Tent map for the random permutation. The high random secret key with a length equal to the size of the audio data is then generated using a 1D logistic map. Finally, the Exclusive OR (XOR) operation is applied between the generated key and the sh

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Publication Date
Fri Jan 01 2021
Journal Name
Ieee Access
Keratoconus Severity Detection From Elevation, Topography and Pachymetry Raw Data Using a Machine Learning Approach
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Publication Date
Fri Jan 01 2016
Journal Name
World Scientific News
Effect of annealing temperature on the structural and optical properties of CdSe: 1% Ag thin films
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Publication Date
Sun Oct 01 2023
Journal Name
Journal Of Taibah University Medical Sciences
Histological evaluation of the effects of bone morphogenetic protein 9 and angiopoietin 1 on bone healing
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Publication Date
Wed Aug 17 2022
Journal Name
Al–bahith Al–a'alami
Women’s Traits In The Iraqi Satirical Television Show ‘State Of Melon’ A Paper Extracted from A Masters Thesis
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The research aims to know the traits or characteristics of woman in terms of her external
appearance, motives for her behavior, feelings, mood and ability.
It, moreover, seeks woman’s relationship with others as it is presented by the Iraqi
satirical television show “ State of Melon “.
The researcher adopted for that survey approach using the method of content analysis
to study the research sample represented by “ State of Melon “ show which was
exposed through the screen of a group of channels:
“Hona Baghdad Satellite Channel, then Asia Satellite Channel, Dijla Satellite Channel,
and UTV Satellite Channel.”For this, the researcher used Margaret Gallagher’s Model to analyze the image of
woman in

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Publication Date
Sat Mar 07 2026
Journal Name
Al–bahith Al–a'alami
Persuasive Sentimental Method in the Electronic Newspapers of Terrorist Organizations - A research drawn from a Master Degree thesis
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The paper probes into minute identification of the data of the methods followed in the electronic newspapers that aim to promote terrorist organizations like Al Qaeda and ISIS to draw emotional empathy and sympathy with them.
The paper aims at identifying:
How emotional empathy was utilized by terrorists in E-newspapers.
How useful utilizing emotional empathy was in attracting supporters. The sample that is used in the paper is based on the opening articles of E-newspapers that propagate Al Qaeda and ISIS, e.g. (Sawtu el jihad) “The Sound of Fighting in the Name of God”, (Mua’skar el Battar wal Shamikha wal Khansaa) “Camps of Al Battar, Shamika, and Khansaa”, “Inspire” and (Thurwatu el Sanam, Dabiq, and Rumiyah)

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Publication Date
Thu Oct 01 2009
Journal Name
Iraqi Journal Of Physics
The Structural and Optical Properties of Hydrogenated and Nitrogenated a-Si0.1Ge0.9 and a-Si0.1Ge0.9:3% B Thin Films
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It is shown that pure and 3% boron doped a-Si0.1Ge0.9:H and a-Si0.1Ge0.9:N thin films
could be prepared by flash evaporation processes. The hydrogenation and nitrogenation
are very successful in situ after depositing the films. The FT-IR analysis gave all the
known absorbing bonds of hydrogen and nitrogen with Si and Ge.
Our data showed a considerable effect of annealing temperature on the structural and
optical properties of the prepared films. The optical energy gap (Eopt.) of a-Si0.1Ge0.9
samples showed to have significant increase with annealing temperature (Ta) also the
refractive index and the real part of dielectric constant increases with Ta, however the
extinction coefficient and imaginary part of dielect

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