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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
Sun Apr 30 2023
Journal Name
Al-kindy College Medical Journal
Prevalence of Burnout Syndrome and its Association with Job Title and Violence among Physicians in Baghdad: A Triangulated Methodology Study
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Background: Economic Globalization affects work condition by increasing work stress. Chronic work stress ended with burnout syndrome.

Objectives: To estimate the prevalence of burnout syndrome and the association of job title, and violence with it among physicians in Baghdad, and to assess the burnout syndrome at patient and work levels by structured interviews.

Subjects and Methods: A cross section study was conducted on Physicians in Baghdad. Sampling was a multistage, stratified sampling to control the confounders in the design phase. A mixed qualitative and quantitative

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Publication Date
Wed Aug 31 2022
Journal Name
F1000research
Inflammatory markers in patients who presented with acute coronary syndrome and history of COVID-19 infection: a cross-sectional study
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Background: During the COVID-19 outbreak, the number of patients who have developed acute coronary syndromes (ACS) has soared rapidly, cardiovascular disease and mortality are influenced by the elevated inflammatory biomarkers. The aim of this study is to compare inflammatory markers between patients with ACS who hadn’t previously had COVID-19 and those who’d be infected within the preceding three months; as well as, evaluating the effect of statins on inflammatory biomarkers.

Methods: This is a comparative cross-sectional study of 42 patients who presented with ACS and had previously had COVID-19 and 48 patient who had never had CO

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Publication Date
Thu Dec 21 2023
Journal Name
Mathematical Modelling Of Engineering Problems
Recovering Time-Dependent Coefficients in a Two-Dimensional Parabolic Equation Using Nonlocal Overspecified Conditions via ADE Finite Difference Schemes
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Publication Date
Fri Jan 01 2021
Journal Name
International Journal Of Nonlinear Analysis And Applications
Big data analysis by using one covariate at a time multiple testing (Ocmt) method: Early school dropout in iraq
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Publication Date
Tue Jun 18 2024
Journal Name
Heat Transfer Engineering
Boosting Solidification Rates in a Triplex-Tube Thermal Storage System Using Circular Fins: Novel Staggered and Inline Fin Arrangements
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Publication Date
Tue May 27 2025
Journal Name
Bulletin Of The Chemical Society Of Ethiopia
Preparation, kinetics, and thermodynamic investigation of Janus green dye removal from aqueous solutions using MnO2 nanoparticles as an adsorbent
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In this study, manganese dioxide (MnO₂) nanoparticles (NPs) were synthesized via the hydrothermal method and utilized for the adsorption of Janus green dye (JG) from aqueous solutions. The effects of MnO₂ NPs on kinetics and diffusion were also analyzed. The synthesized NPs were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), energy-dispersive X-ray analysis (EDX), and Fourier-transform infrared spectroscopy (FT-IR), with XRD confirming the nanoparticle size of 6.23 nm. The adsorption kinetics were investigated using three models: pseudo-first-order (PFO), pseudo-second-order (PSO), and the intraparticle diffusion model. The PSO model provided the best fit (R² = 0.999), indicating that the adsorpti

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Publication Date
Thu Feb 01 2024
Journal Name
Journal Of Engineering
Evaluating the Knowledge for Integrating RM and VM Using BIM in the Iraqi Construction Sector
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The construction industry plays a crucial role in the countries' economy, especially in the developed country. This point encourages the concerned institution to use new techniques and integrate many techniques and methods to maximize the benefits. The main objective of this research is to evaluate the use of risk management, value management, and building information modeling in the Iraqi construction industry. The evaluation process aims at two objectives. The direct objective was to evaluate the knowledge in risk management (RM), value management (VM), and building information modeling (BIM). The indirect objective was to support the participants with information related to the main items mentioned. The questionnaire

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Publication Date
Sun Oct 01 2023
Journal Name
Baghdad Science Journal
Nonlinear Ritz Approximation for the Camassa-Holm Equation by Using the Modify Lyapunov-Schmidt method
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          In this work, the modified Lyapunov-Schmidt reduction is used to find a nonlinear Ritz approximation of Fredholm functional defined by the nonhomogeneous Camassa-Holm equation and Benjamin-Bona-Mahony. We introduced the modified Lyapunov-Schmidt reduction for nonhomogeneous problems when the dimension of the null space is equal to two.  The nonlinear Ritz approximation for the nonhomogeneous Camassa-Holm equation has been found as a function of codimension twenty-four.

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
The eloquence of the poetic image in the poetry of the Andalusian son of Labanism is a stylistic approach
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The resort to the eloquence of the poetic image as a style reveals the poet's creativity and creativity in dealing with external influences, and reflect them with emotional images express a sense of intense emotional imagination, and this imagination stems from the experience of a poetic sense of truth, tasted by the recipient before the creator of the poetic text.

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Publication Date
Tue Oct 18 2022
Journal Name
Journal Of Research In Medical And Dental Science
Assessment of Salivary Macrophage Inflammatory Protein-1 Alpha Level in Different Stages of Periodontitis
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Assessment of Salivary Macrophage Inflammatory Protein-1 Alpha Level in Different Stages of Periodontitis, Riyam Muthanna Muhammed*, Hadeel Mazin Akram

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