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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 Feb 25 2017
Journal Name
International Journal On Advanced Science, Engineering And Information Technology
A Novel DNA Sequence Approach for Network Intrusion Detection System Based on Cryptography Encoding Method
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A novel method for Network Intrusion Detection System (NIDS) has been proposed, based on the concept of how DNA sequence detects disease as both domains have similar conceptual method of detection. Three important steps have been proposed to apply DNA sequence for NIDS: convert the network traffic data into a form of DNA sequence using Cryptography encoding method; discover patterns of Short Tandem Repeats (STR) sequence for each network traffic attack using Teiresias algorithm; and conduct classification process depends upon STR sequence based on Horspool algorithm. 10% KDD Cup 1999 data set is used for training phase. Correct KDD Cup 1999 data set is used for testing phase to evaluate the proposed method. The current experiment results sh

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Publication Date
Fri Mar 20 2020
Journal Name
Remote Sensing
Lossy and Lossless Video Frame Compression: A Novel Approach for High-Temporal Video Data Analytics
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The smart city concept has attracted high research attention in recent years within diverse application domains, such as crime suspect identification, border security, transportation, aerospace, and so on. Specific focus has been on increased automation using data driven approaches, while leveraging remote sensing and real-time streaming of heterogenous data from various resources, including unmanned aerial vehicles, surveillance cameras, and low-earth-orbit satellites. One of the core challenges in exploitation of such high temporal data streams, specifically videos, is the trade-off between the quality of video streaming and limited transmission bandwidth. An optimal compromise is needed between video quality and subsequently, rec

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Publication Date
Wed Jan 01 2025
Journal Name
Biomaterials Science
Single-atom silver-borophene hybrid hydrogels for electrically stimulated wound healing: a multifunctional antibacterial platform
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Publication Date
Mon Apr 23 2018
Journal Name
Ibn Al- Haitham Journal For Pure And Applied Science
Performance of Strelitzia reginae Flowers Dye as Sensitizer for New Dye-Sensitized Solar Cell Fabrication
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        In current study, the dye from flowers petals of Strelitzia reginae used for the first time to prepare natural photosensitizer for DSSC fabrication. Among five different solvents used to extract the natural dye from S. reginae flowers, the ethanol extract of anthocyanin dye revealed higher absorption spectrum of 0.757a.u. at wavelength of 454nm.  A major effect of temperature was studied to increase the extraction yield. The results show that the optimal temperature was 70 °C and there was a sharp decrease of dye concentration from 0.827 at temperature of 70 °C to 0.521 at temperature of 90°C. The extract solution of flowers of S. reginae showed higher concentration in acidic media, especially at pH 4 (0.902). The

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Publication Date
Tue Mar 12 2019
Journal Name
Lubricants
Absorption Wavebands for Discriminating Oxidation Time of Engine Oil as Detected by FT-IR Spectroscopy
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Fourier Transform-Infrared (FT-IR) spectroscopy was used to analyze gasoline engine oil (SAE 5W20) samples that were exposed to seven different oxidation times (0 h, 24 h, 48 h, 72 h, 96 h, 120 h, and 144 h) to determine the best wavenumbers and wavenumber ranges for the discrimination of the oxidation times. The thermal oxidation process generated oil samples with varying total base number (TBN) levels. Each wavenumber (400–3900 cm−1) and wavenumber ranges identified from the literature and this study were statistically analyzed to determine which wavenumbers and wavenumber ranges could discriminate among all oxidation times. Linear regression was used with the best wavenumbers and wavenumber ranges to predict oxidation time.

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Publication Date
Tue Mar 19 2024
Journal Name
Birth
Changes in attitudes to childbirth in modern times illustrated over three generations in Iraq
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Abstract<sec><title>Objective

To describe changes in attitudes and expectations of labor over the previous six decades, comparing the Iraqi generation who labored at home without medical assistance with their descendants.

Study Design

We used semi‐structured telephone interviews with 22 women across three generations of one extended family living and giving birth in Iraq between the 1950s and the 2010s. Qualitative data were analyzed thematically using open, axial, and selective coding.

Results

Each generation experienced a paradigm shift in childbirth, from exclus

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Publication Date
Tue Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
Employing the indicators of stereotypes and the dimensions of organizational clarity and their role in achieving the planned organizational behavior Analytical study on a sample of workers in some departments of the Faculties of Engineering, University of
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The current research examines the employment of indicators of stereotypes and the dimensions of organizational clarification to achieve planned organizational behaviour on a sample of employees in a number of departments of the Faculties of Engineering, University of Kufa, for a sample of (122) teaching staff. This research proposes the use of positive indicators of stereotypes for both the organization and employees and their awareness of what they want to obtain and what should be done for both parties and the removal of organizational clarity represented by the functional dimension that explores to what degree the employee's understanding of the internal strategy of the organization and the strategic dimension that searches fo

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Publication Date
Thu Aug 21 2025
Journal Name
Journal Of Health And Biology
Distribution and Species Diversity of the Dove Genus Streptopelia: A Systematic Review
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Some species, such as the Eurasian Collared-Dove (S. decaocto) are fast expanding around the planet, while others, such as the European Turtle-Dove (S. turtur), are experiencing precipitous population declines. Climate change, habitat loss, greater cultivated areas, and hunting pressure are the major threats to the diversity of Streptopelia. A few species require urgent conservation action. Priority for subsequent research should be to redress outstanding taxonomic uncertainties, ascertain the effect of climate change on distributions, and put in place conservation measures for declining taxa. We provide here a detailed review on how it is possible to understand the diversity of Streptopelia and how such an understanding can con

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Publication Date
Mon Dec 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The political violence risk insurance A possibility of its application in Iraq
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Iraqi insurance market need to develop products and to find new insurance policies to cover the damages of the violence and political commotions dangers and to meet the needs of the proposers.                                       

 The global insurance companies recently issued such policies to pay the losses wich caused by the violent political acts of vandalism suffered by the property and investments wich estimated billions of dollars.                

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Publication Date
Sun Jun 30 2024
Journal Name
International Journal Of Pharmaceutical Sciences And Nanotechnology(ijpsn)
A Subject Review on Application of Analytical Chemistry in the Mitochondrial Medicine
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Understanding energy metabolism and intracellular energy transmission requires knowledge of the function and structure of the mitochondria. Issues with mitochondrial morphology, structure, and function are the most prevalent symptoms. They can damage organs such as the heart, brain, and muscle due to a variety of factors, such as oxidative damage, incorrect metabolism of energy, or genetic conditions. The control of cell metabolism and physiology depends on functional connections between mitochondrial and biological surroundings. Therefore, it is essential to research mitochondria in situ or in vivo without isolating them from their surrounding biological environment. Finding and spotting abnormal alterations in mitochondria is the

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