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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 Jan 01 2019
Journal Name
Journal Of Global Pharma Technology
A morphological study and a new species registration of genus Xerophloea Germa, 1839 sp.nov. From sub-family Ledrinae Fairmai, 1855 of the leafhopper (Hemiptera: Cicadellidae) in Iraq
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Publication Date
Fri Apr 30 2021
Journal Name
Al-kindy College Medical Journal
Immunological aspects of Alpha 1 Antitrypsin in COVID-19 infection among the Populace and Pregnant Women: Alpha 1 Antitrypsin and COVID-19
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Since the COVID-19 pandemic alarm was made by the severe acute respiratory syndrome (SARS)-coronavirus (CoV) 2, several institutions and agencies have pursued to clarify the viral virulence and infectivity. The fast propagation of this virus leads to an unprecedented rise in the number of cases worldwide. COVID-19 virus is exceptionally contagious that spreads through droplets, respiratory secretions, and direct contact. The enveloped, single-stranded RNA virus has a specific envelop region called (S) region encoding (S protein) that specifically binds to the host cell receptor. Viral infection requires receptors' participation on the host cell membrane's surface, a  key- step for the viral invasion of susceptible cells.

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Publication Date
Sat Jan 01 2022
Journal Name
The International Journal Of Nonlinear Analysis And Applications
Developing Bulk Arrival Queuing Models with Constant Batch Policy Under Uncertainty Data Using (0-1) Variables
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This paper delves into some significant performance measures (PMs) of a bulk arrival queueing system with constant batch size b, according to arrival rates and service rates being fuzzy parameters. The bulk arrival queuing system deals with observation arrival into the queuing system as a constant group size before allowing individual customers entering to the service. This leads to obtaining a new tool with the aid of generating function methods. The corresponding traditional bulk queueing system model is more convenient under an uncertain environment. The α-cut approach is applied with the conventional Zadeh's extension principle (ZEP) to transform the triangular membership functions (Mem. Fs) fuzzy queues into a family of conventional b

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Publication Date
Tue Jul 09 2024
Journal Name
Diagnostics
A Novel Hybrid Machine Learning-Based System Using Deep Learning Techniques and Meta-Heuristic Algorithms for Various Medical Datatypes Classification
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Medicine is one of the fields where the advancement of computer science is making significant progress. Some diseases require an immediate diagnosis in order to improve patient outcomes. The usage of computers in medicine improves precision and accelerates data processing and diagnosis. In order to categorize biological images, hybrid machine learning, a combination of various deep learning approaches, was utilized, and a meta-heuristic algorithm was provided in this research. In addition, two different medical datasets were introduced, one covering the magnetic resonance imaging (MRI) of brain tumors and the other dealing with chest X-rays (CXRs) of COVID-19. These datasets were introduced to the combination network that contained deep lea

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Publication Date
Sat Jan 27 2024
Journal Name
History Of Medicine
Developing and Validating a Spectrophotometric Method for Estimating Antifungal (Nystatin) in its Pure Form Pharmaceutical Formulation Using Tetrachloro-1,4 benzoquinone
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The UV−VIS absorption spectroscopy technique was used to study the formation of a new complex of charge transfer (CT) between bioactive organic molecules as (Nystatin) containing both a π-electrons from a conjugated system and lone-pair of electrons (amine) with Tetrachloro-1,4 benzoquinone (TCBQ) as a π-acceptor in which the transferred electron goes into its vacant anti-bonding molecular orbitals. The Tyrian purple-colored complex formed was quantitatively measured at 544 nm. This complex shows obeying Beer's law within the concentration range of (10-90) μg.ml-1The stoichiometry of the formed complex between the (Nys.) and (TCBQ) was found 1:2 as evaluated by continuous variation (Job's method) and mole ratio method The value of mola

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Publication Date
Mon Mar 01 2021
Journal Name
Iraqi Journal Of Physics
Studying the Correlation Between Supermassive Black Holes and Star Formation Rate for Samples of Seyfert Galaxies (Type 1 and 2)
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An optical spectroscopic study is reported in this article to study the correlation between the supermassive black hole (SMBH) and the star formation rate (SFR) for a sample of Seyfert galaxies type (I and II). The study focused on 45 galaxy of Seyfert 1, in addition to 45 galaxy of Seyfert 2, where these samples have been selected form different survey of Salon Digital Sky Survey (SDSS). The redshift (z) of these objects were between (0.02 – 0.26). The results of Seyfert 1 galaxies shows that there good correlation between the SMBH and the SFR depending on statistical analysis parameter named Spearman’s Rank Correlation in a factor of (ρ=0.609), as well as the Seyfert 2 galaxies results show a good correlation between the SMBH

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Publication Date
Mon Mar 01 2021
Journal Name
Iraqi Journal Of Physics
Studying the Correlation Between Supermassive Black Holes and Star Formation Rate for Samples of Seyfert Galaxies (Type 1 and 2)
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An optical spectroscopic study is reported in this article to study the correlation between the supermassive black hole (SMBH) and the star formation rate (SFR) for a sample of Seyfert galaxies type (I and II). The study focused on 45 galaxy of Seyfert 1, in addition to 45 galaxy of Seyfert 2, where these samples have been selected form different survey of Salon Digital Sky Survey (SDSS). The redshift (z) of these objects were between (0.02 – 0.26). The results of Seyfert 1 galaxies shows that there good correlation between the SMBH and the SFR depending on statistical analysis parameter named Spearman’s Rank Correlation in a factor of (ρ=0.609), as well as the Seyfert 2 galaxies results show a good correlation between the SMBH and

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Engineering
A STUDY OF THE EFFECT OF SEMI-ANGLE OF CONE ON THE VIBRATION CHARACTERISTICS OF CYLINDRICAL-CONICAL COUPLED SHELL STRUCTURE
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In this work, the effect of variation of semi-angle of the conical part on the vibration characteristics of cylindrical-conical coupled structure is investigated. The shell is made of polyester resin reinforced by continuous E-glass fibers. The case is analyzed experimentally and numerically for orthotropic shell structures. The experimental program is conducted by exciting the fabricated structure by an impact hammer and monitoring the response using an attached accelerometer for different semi-angles of the conical part.
Software named SIGVIEW is used to perform the signal processing on the acquired signal in order to measure the natural frequencies and the corresponding mode shapes. The numerical investigation is achieved using ANS

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Publication Date
Fri Apr 01 2016
Journal Name
Al–bahith Al–a'alami
Journalism of Paper Newspapers in Light of the Competition of the Electronic Press / (A Field Study of Yemeni Daily Newspapers)
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The researcher seeks to get scientific facts through knowing the relationship between the priorities of Yemeni audience in follow-up paper daily newspapers compared to surfing publics the online journalism sites and the nature of information obtained from online journalism sites and printed paper newspapers and the impact of the daily newspapers in the priority of issues and political events among a sample of a group of Yemeni readers in order to identify the extent to keep up the paper daily newspapers of the development in the field of online journalism and the extent of reading paper newspapers under the intense competition by online journalism sites, and are paper newspapers able to keep pace with the actual developments provided by

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Publication Date
Wed Aug 01 2012
Journal Name
I-manger's Journal On Information Technology
A MODULE FOR ENHANCING RECOGNITION SYSTEM FOR QR CODE SCANNED IMAGE
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A QR code is a type of barcode that can hold more information than the familiar kind scanned at checkouts around the world. The “QR” stands for “Quick Response”, a reference to the speed at which the large amounts of information they contain can be decoded by scanners. They are being widely used for advertising campaigns, linking to company websites, contest sign-up pages and online menus. In this paper, we propose an efficient module to extract QR code from background and solve problem of rotation in case of inaccurate image taken from mobile camera.