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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
Mon Feb 10 2025
Journal Name
Aip Conference Proceedings
Development of an HPLC method for the determination of tramadol hydrochloride using ZIC-HILIC columns
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Publication Date
Fri Jul 19 2024
Journal Name
Baghdad Science Journal
Study of the Relationship for Neutron and Proton Skin Thickness on the Neutron Equation of State for 18Ne-18O Pair Mirror Nuclei
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في إطار نموذج القشرة، تم اعتماد الدوال الموجية أحادية الجسيم لتقريب هاتري - فوك مع تفاعلات سكيرم  مثل Skxtb, Skxs25, , Sly4وBsk9 لحساب سمك القشرة النيوتروني، ونصف قطر المرآتي ونصف قطر الشحنة المرآتية ، لزوج النوى المرآتية 18Ne-18O. تم حساب الدوال الموجية باستخدام كود نموذج القشرة NuShellX@MSU. تتأثر القيم المحسوبة لجذر متوسط ​نصف القطر المربع بنوع التفاعلات المستخدمة. كما تم تحديد طاقة التناظر وانحدارها عند كثافة التشبع الن

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Publication Date
Fri Jul 19 2024
Journal Name
Baghdad Science Journal
Study of the Relationship for Neutron and Proton Skin Thickness on the Neutron Equation of State for 18Ne-18O Pair Mirror Nuclei
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Within the framework of the shell model, the single-particle wave functions of Hartree-Fock approximation adopted with Skyrme interactions like kxtb, Skxs25, Sly4 and Bsk9 to get the thickness of the neutron skin, the mirror radii and the charges mirror radii for 18Ne-18O pair mirror nucleus. The wave functions were calculated using the NuShellX@MSU shell model code. The computed values of root-mean-square-radii are inuenced by the type of interaction employed. The symmetry energy and its slope at nuclear saturation density and the mirror energy displacement were also determined. Comparisons between theoretical and experimental data were made and it was concluded that the data are well described in of this pair mirror nucleus

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Publication Date
Mon Mar 01 2021
Journal Name
Journal Of Physics: Conference Series
The Bifurcation Analysis and Persistence of the Food Chain Ecological Model with Toxicant
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Abstract<p>In this work, the occurrence conditions of both local Bifurcation and persistence were studied, Saddle-node bifurcation appears near fourth point, near the first point, the second point and the third point a transcritical bifurcation occurred but no pitchfork bifurcation happened near any of the four equilibrium points. In addition to study conditions for Hopf-bifurcation near positive stable point that is the fourth point. Besides discuss persistence occurrence as globally property of the food chain of three species include prey, first predator and top predator with impact of toxin in all species and harvesting effect on the predator’s only. Numerical results for the set of hypothe</p> ... Show More
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Publication Date
Sun Nov 01 2015
Journal Name
Journal Of Dentistry
New functional and aesthetic composite materials used as an alternative to traditional post materials for the restoration of endodontically treated teeth
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Objectives To tailor composites of polyethylene–hydroxyapatite to function as a new intracanal post for the restoration of endodontically treated teeth (ETT). Methods Silanated hydroxyapatite (HA) and zirconium dioxide (ZrO2) filled low-density polyethylene (LDPE) composites were fabricated by a melt extrusion process and characterised using infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA). The flexural strength and modulus were determined in dry state and post ageing in simulated body fluid and fractured surfaces analysed by SEM. The water uptake and radiographic appearance of the experimental composites were also measured and compared with a commercially known endodontic fibre

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Publication Date
Fri Nov 24 2017
Journal Name
Journal Of Engineering
A new analytic method to tune a fractional order PID controller
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This paper proposes a new method to tune a fractional order PID controller. This method utilizes both the analytic and numeric approach to determine the controller parameters. The control design specifications that must be achieved by the control system are gain crossover frequency, phase margin, and peak magnitude at the resonant frequency, where the latter is a new design specification suggested by this paper. These specifications results in three equations in five unknown variables. Assuming that certain relations exist between two variables and discretizing one of them, a performance index can be evaluated and the optimal controller parameters that minimize this performance index are selected. As a case study, a third order linear time

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Publication Date
Fri Nov 24 2017
Journal Name
Journal Of Engineering
A New Analytic Method to Tune a Fractional Order PID Controller
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This paper proposes a new method to tune a fractional order PID controller. This method utilizes both the analytic and numeric approach to determine the controller parameters. The control design specifications that must be achieved by the control system are gain crossover frequency, phase margin, and peak magnitude at the resonant frequency, where the latter is a new design specification suggested by this paper. These specifications results in three equations in five unknown variables. Assuming that certain relations exist between two variables and discretizing one of them, a performance index can be evaluated and the optimal controller parameters that minimize this performance index are selected. As a case study, a thir

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Publication Date
Tue Jul 01 2025
Journal Name
Journal Of Breast Diseases
Association Between Serum Interleukin-41 Levels and Breast Cancer Status: A Case–Control Study in Iraqi Women
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Publication Date
Fri Jan 15 2021
Journal Name
Psychology And Education Journal
Property and Possession in Gayl Jones’s Novel Corregidora: A Study in African American Literature and Literary Theory
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the traumatic memory of their ancestors. The novel navigates sites of trauma, memory, and blues music while resisting the bourgeoisie-capitalist relationships that permeated not only white society but also African American communities. Jones’s novel presents the plight of an African American woman, Ursa, caught between the memory of her enslaved foremothers and her life in an emancipated world. The physical and spiritual exploitation of African American women who bear witness to the history of slavery in Corregidora materializes black women’s individuality. This article is framed by trauma studies as well as the Marxists’ concepts of commodification, accumulation, and production. Ursa, one of the Corregidora women, represents

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Publication Date
Tue Jun 28 2022
Journal Name
Research Journal Of Pharmacy And Technology
A Case-control Study to Determine Metalloproteinase-12 and Lysyl Oxidase Levels in Iraqi women with Osteoporosis
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The current study aimed to ascertain the levels of matrix metalloproteinase-12 (MMP-12) and Lysyl oxidase (LOX) in osteoporosis patients and their correlation with alkaline phosphatase (ALP), magnesium (Mg), vitamin D (Vit D), calcium (Ca), phosphorus (P), and T-score %. 110 participants recruited from Baghdad Teaching Hospital, Iraq, were enrolled in this study from November 2019 to March 2020). The participants were divided into two groups: Group 1 comprised 60 osteoporotic women and group 2 consisted of 50 healthy women. (MMP and LOX) were estimated using a quantitative enzyme-linked immunosorbent assay (ELISA. The results showed significant differences in serum LOX, age, ALP, Mg, and T-score %, while no significant differences i

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