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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
Thu Sep 01 2022
Journal Name
Iraqi Journal Of Physics
Calculation of the Magnetic Dipole and Electric Quadrupole Moments of some Sodium Isotopes using Shell Model with Skyrme Interaction
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         In the present work, the magnetic dipole and electric quadrupole moments for some sodium isotopes have been calculated using the shell model, considering the effect of the two-body effective interactions and the single-particle potentials. These isotopes are; 21Na (3/2+), 23Na (3/2+), 25Na (5/2+), 26Na (3+), 27Na (5/2+), 28Na (1+) and, 29Na (3/2+). The one-body transition density matrix elements (OBDM) have been calculated using the (USDA, USDB, HBUMSD and W) two-body effective interactions carried out in the sd-shell model space. The sd shell model space consists of the active 2s1/2, 1d5/2,

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Publication Date
Thu Apr 25 2019
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
The Correlation between the Dimensions of Organizational Silence and the F Function Life an Exploratory Study of the Views of a Sample of Workers in the Health Center / Sulaykh: The Correlation between the Dimensions of Organizational Silence and the F Function Life an Exploratory Study of the Views of a Sample of Workers in the Health Center / Sulaykh
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The research aims to test the effect of the behavioral factors (intangible) represented by an explanatory variable represented by organizational silence and a responsive variable of quality of Function life. The problem was the negative effects of the organizational silence on the morale of the employees and consequently their performance and the quality of function life. To collect the data and information needed to measure the two variables of research conducted in the health center / Sulaikh by taking a sample of (40) employees to test the hypotheses of research through the survey of their views, using statistical tools non parametric using the program. The most important recommendations were the establishment of training workshops fo

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Publication Date
Fri Jan 19 2024
Journal Name
Research Journal Of Pharmacy And Technology
Serum Levels of Fetuin-A, Ischemia-modified Albumin (IMA), and Ferritin in Hospitalized patients with severe COVID-19. A Case-control Study
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Objective: To measure the serum levels of Fetuin-A, ischemia-modified albumin (IMA), and ferritin in hospitalized patients with severe COVID-19in Baghdad, Iraq. Moreover, to determine these biomarkers' cut-off valuesthat differentiate between severely ill patients and control subjects. Methods: This case-control study was done from 15 September to the end of December 2021 and involved a review of the files and collectionof blood samples from patients (n=45, group1) hospitalized in COVID-19 treatment centersbecause of severe symptoms compared tohealthy subjects as controls (n=44, group2). Results: Fetuin-A serum levels were not statistically different between patients and controls. In contrast, IMA and ferritin levels were significan

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Publication Date
Fri Jan 01 2021
Journal Name
Tigris And Euphrates Rivers: Their Environment From Headwaters To Mouth
Ornamental Fishes: A Looming Danger for Inland Fish Diversity of Iraq
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Publication Date
Fri Apr 25 2025
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences (ihjpas)
Spectrophotometric Investigations for Simultaneous Analysis of Certain Antibacterial: A Brief Review
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Antibacterial substances belong to a group of compounds that attack dangerous microorganisms. Therefore, killing bacteria or reducing their metabolic activity will lessen their adverse effects on a biological system. They originated from either synthetic materials, microbes, or mold. Many of these medications treat the gram-negative bacteria from the critical precedence group, such as pseudomonas, carbapenem-resistant acinetobacter, and enterobacterales. This study aims to investigate the simultaneous analysis of specific antibacterial spectrophotometrically. The WHO maintains this list of priority infections with antibiotic resistance. Drug combinations in single dosage forms are becoming increasingly popular in the pharmaceutical industry

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Publication Date
Fri Sep 06 2024
Journal Name
Journal Of Optics
Synthesis of N-A cysteine-capped CdTe QDs for optical biosensing
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In this investigation, water-soluble N-Acetyl Cysteine Capped-Cadmium Telluride QDs (NAC/CdTe nanocrystals), utilizing N-acetyl cysteine as a stabilizer, were prepared to assess their potential in differentiating between DNA extracted from pathogenic bacteria (e.g. Escherichia coli isolated from urine specimen) and intact DNA (extracted from blood of healthy individuals) for biomedical sensing prospective. Following the optical characterization of the synthesized QDs, the XRD analysis illustrated the construction of NAC-CdTe-QDs with a grain size of 7.1 nm. The prepared NAC-CdTe-QDs exhibited higher PL emission features at of 550 nm and UV-Vis absorption peak at 300 nm. Additionally, the energy gap quantified via PL and UV–Vis were 2.2 eV

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Publication Date
Thu Dec 01 2016
Journal Name
2016 Ieee Symposium Series On Computational Intelligence (ssci)
A fusion of time-domain descriptors for improved myoelectric hand control
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Publication Date
Sun Jun 06 2010
Journal Name
Baghdad Science Journal
Charge density distributions for odd-A of 2s-1d shell nuclei
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An analytical expression for the charge density distributions is derived based on the use of occupation numbers of the states and the single particle wave functions of the harmonic oscillator potential with size parameters chosen to reproduce the observed root mean square charge radii for all considered nuclei. The derived expression, which is applicable throughout the whole region of shell nuclei, has been employed in the calculations concerning the charge density distributions for odd- of shell nuclei, such as and nuclei. It is found that introducing an additional parameters, namely and which reflect the difference of the occupation numbers of the states from the prediction of the simple shell model leads to obtain a remarkabl

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Publication Date
Wed Oct 12 2022
Journal Name
Axioms
Razy: A String Matching Algorithm for Automatic Analysis of Pathological Reports
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Pathology reports are necessary for specialists to make an appropriate diagnosis of diseases in general and blood diseases in particular. Therefore, specialists check blood cells and other blood details. Thus, to diagnose a disease, specialists must analyze the factors of the patient’s blood and medical history. Generally, doctors have tended to use intelligent agents to help them with CBC analysis. However, these agents need analytical tools to extract the parameters (CBC parameters) employed in the prediction of the development of life-threatening bacteremia and offer prognostic data. Therefore, this paper proposes an enhancement to the Rabin–Karp algorithm and then mixes it with the fuzzy ratio to make this algorithm suitable

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Publication Date
Fri May 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
A review of ultra-high temperature materials for thermal protection system
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Abstract<p>Ultra-High Temperature Materials (UHTMs) are at the base of entire aerospace industry; these high stable materials at temperatures exceeding 1600 °C are used to manage the heat shielding to protect vehicles and probes during the hypersonic flight through reentry trajectory against aerodynamic heating and reducing plasma surface interaction. Those materials are also recognized as Thermal Protection System Materials (TPSMs). The structural materials used during the high-temperature oxidizing environment are mainly limited to SiC, oxide ceramics, and composites. In addition to that, silicon-based ceramic has a maximum-use at 1700 °C approximately; as it is an active oxidation process o</p> ... Show More
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