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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 Dec 01 2013
Journal Name
Baghdad Science Journal
Theoretical Study of Charge Transfer in Styryl Thiazilo Quinoxaline Dyes STQ-1, STQ-2,and STQ-3 in Organic Media System
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Charge transfer in styryl dyes STQ-1, STQ-2,and STQ-3 with organic media system has been studied theoretically depending on the Franck- Condon rule and continuum dielectric model . The reorientation energies (eV) were evaluated theoretically depending on dipole momentum, dielectric constant , and refrective index n. The rate constant of charge transfer has been calculated depending on the reorientation energy (eV) ,effective free energy , potential height barrier , and coupling coefficient . A matlap program has been written to calculated the rate constant of charge transfer and other parameter. The results of calculations show that STQ-2 dye is more reaction for charge transfer compare with STQ-1 and STQ-3 dyes

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Publication Date
Sat Sep 02 2017
Journal Name
Dissertation
Integrating Biophysical and Socio-Economic Approaches to Identify Suitable Policy Incentives for Enhancing Sustainable Water and Land Use (WLI project a case study of Iraq)
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Publication Date
Wed Jan 15 2025
Journal Name
International Endodontic Journal
Fabrication and characterization of 3D-printed polymeric‐based scaffold coated with bioceramic and naringin for a potential use in dental pulp regeneration (in vitro study)
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3D‐printed scaffolds loaded with healing directed agents could be employed for better treatment outcome in regenerative dentistry. The aim of this study was to fabricate and characterize simple 3D‐printed poly lactic acid (PLA) scaffolds coated with nanoHydroxyapatite (nHA), Naringin (NAR), or their combination, and testing their morphological, chemical, mechanical, antibacterial, biocompatible and bioactive properties. Methodology: Two variants pore sizes, 300 and 700 μm, of 3D‐printed PLA disc scaffolds measuring (10 × 1 mm) were fabricated. These scaffolds were dip‐coated with nHA, NAR, or both (nHA/NAR). Field emission scanning electron microscopy (FeSEM), energy‐dispersive X‐ray spectroscopy (EDX), Fourier transfo

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Publication Date
Sun Feb 22 2026
Journal Name
Clinical Drug Investigation
A Field-Based Cost-Effectiveness Study of Aflibercept and Bevacizumab in Treat-and-Extend Versus Pro Re Nata Protocols for Diabetic Macular Edema in Iraq
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Publication Date
Tue Mar 19 2024
Journal Name
Jordan Journal Of Pharmaceutical Sciences
MMP-1 and MMP-7 Expression is Influenced by Ginsenosides in Mice Exposed to Aflatoxin B1: in vivo Study
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Panax ginseng (PG), one of the most widely used herbal medicines, has demonstrated various beneficial effects such as anti-inflammatory, antioxidant, and anticancer impacts. Naturally occurring ginsenosides in the ginseng plant inhibit cell proliferation and significantly reduce liver damage induced by certain chemicals. Aflatoxin B1 (AFB1) is a primary mycotoxin due to its hepatotoxic, immunotoxic, and oncogenic effects in animal models and humans. In this study, we examined the effects of assorted doses of PG aqueous crude extract on the expression of matrix metalloproteinase 1 and 7 (MMP-1 and MMP-7) in the kidney, spleen, and liver of experimental AFB1-exposed mice, using immunohistochemistry (IHC). Mice were orally administered

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Publication Date
Sun Dec 01 2002
Journal Name
Iraqi Journal Of Physics
Study of Gamma — irradiation effects on the Polymethylmethacrylate (PMMA) Using (PAL) Method
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Gamma - irradiation effect on polymethylmethacrylate (PMMA) samples has been studied using Positron Annihilation Lifetime (PAL) method. The orthopositronium (o-Ps) lifetime τ3, hence the o-ps parameters, the volume hole size (Vh) and the free volume fraction (Ꞙh) in the irradiated samples were measured as a function of gamma-irradiation dose up to 28.05 kGy. It has been shown that τ 3, Vh, and Ꞙh, are increasing in general with increasing gamma-dose, to reach a maximum percentage increment of 22.42% in τ3, 60% in Vh and 29.5% in Ꞙh, at. 2.55 kGy, whereas τ2 reaches maximum increment of 119. 7% at 7.65 kGy. The results s

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Publication Date
Tue Mar 03 2026
Journal Name
Journal Of Physical Education
Special Exercises Using A Proposed Training Apprentice And Its Effect On Some Biomechanical Indicators and Achieving 110m Hurdles For players Under 20 years old
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Publication Date
Tue Sep 15 2020
Journal Name
Al-academy
Feminist Lament and its Representations in Contemporary Arab Theatrical Text " Al-Khansaa' Play- A Model": نزار شبيب كريم-زينب نوري هاشم
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  The research addresses the feminist lament and its representations in the contemporary Arab theatrical text as one of the purposes of the Arabic poetry and its images, samples, and reasons developed and its incentives multiplied through different time periods in which a dramatic image and representations have been manifested that harmonized with the art of theatre. In order to shed light on these representations, this study has come to look for the representations of lament phenomenon in the Arab theatre texts.
The study consists of an introduction in which the two researchers put forward the research problem, significance and objectives, and a theoretical framework which tackles a theoretical foundation for the research consi

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Publication Date
Sun Mar 06 2016
Journal Name
Baghdad Science Journal
A Note on the Perturbation of arithmetic expressions
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In this paper we present the theoretical foundation of forward error analysis of numerical algorithms under;• Approximations in "built-in" functions.• Rounding errors in arithmetic floating-point operations.• Perturbations of data.The error analysis is based on linearization method. The fundamental tools of the forward error analysis are system of linear absolute and relative a prior and a posteriori error equations and associated condition numbers constituting optimal of possible cumulative round – off errors. The condition numbers enable simple general, quantitative bounds definitions of numerical stability. The theoretical results have been applied a Gaussian elimination, and have proved to be very effective means of both a prior

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Publication Date
Mon Sep 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
The New Synthesis of Potassium-Exchange Zeolite A
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