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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
Australian Journal Of Mathematical Analysis And Applications
Formulation of approximate mathematical model for incoming water to some dams on Tigris and Euphrates Rivers using spline function
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n this paper, we formulate three mathematical models using spline functions, such as linear, quadratic and cubic functions to approximate the mathematical model for incoming water to some dams. We will implement this model on dams of both rivers; dams on the Tigris are Mosul and Amara while dams on the Euphrates are Hadetha and Al-Hindya.

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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
Spectrophotometric Determination of Micro Amount of Chromium (III) Using Sodium 4-((4,5-diphenyl-imidazol-2-yl)diazenyl)-3-hydroxynaphthalene-1-sulfonate in the Presence of Surfactant, Study of Thermodynamic Functions and Their Analytical Applications
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          Using sodium4-((4,5-diphenyl-imidazol-2-yl)diazenyl)-3-hydroxynaphthalene-1-sulfonate (SDPIHN) as a chromogenic reagent in presence of non-ionic surfactant (Triton x-100) to estimate the chromium(III)  ion if the wavelength of this reagent 463 nm to form a dark greenish-brown complex in wavelength 586 nm at pH=10,the complex was stable for longer than 24 hours. Beer's low, molar absorptivity 0.244×104L.mol-1.cm-1, and Sandal's sensitivity 0.021 µg/cm2 are all observed in the concentration range 1-11 µg/mL. The limits of detection (LOD) and limit of quantification (LOQ), respectively, were 0.117 µg/mL and 0.385µg/mL. (mole ratio technique, job's method) were employed to

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Publication Date
Thu Sep 01 2016
Journal Name
Journal Of Ocular Pharmacology And Therapeutics
Formulation and<i>In Vitro</i>Evaluation of Cyclosporine-A Inserts Prepared Using Hydroxypropyl Methylcellulose for Treating Dry Eye Disease
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Publication Date
Mon Aug 05 2024
Journal Name
Pharmacia
A validated spectrophotometric analysis for simultaneous estimation of vincristine sulfate and bovine serum albumin in pure preparations using Vierordt’s method
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The novel Vierordt’s approach, or simultaneous equation method, was created and validated for the concurrent determination of vincristine sulfate (VCS) and bovine serum albumin (BSA) in pure solutions utilizing UV spectrophotometry. It is simple, precise, economical, rapid, reliable, and accurate. This method depends on measuring absorbance at two wavelengths, 296 nm and 278 nm, which correspond to the λmax of VCS and BSA in deionized water, respectively. The calibration curves of VCS and BSA are linear at concentration ranges of 10–60 μg/mL and 200–1600 μg/mL, with correlation coefficient values (R2) of 1 and 0.999, respectively. The limits of detection (LOD) and quantification (LO

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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of Medicine And Life
Antimicrobial photodynamic therapy using a low-power 650 nm laser to inhibit oral Candida albicans activity: an in vitro study
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Publication Date
Sun Feb 08 2026
Journal Name
Journal Of Baghdad College Of Dentistry
The effect of autologous bone marrow-derived stem cells with estimation of molecular events on tooth socket healing in diabetic rabbits (Immunohistochemical study)
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Background: Healing of a tooth extraction socket is a complex process involving tissue repair and regeneration. It involves chemotaxis of appropriate cells into the wound, Transformation of undifferentiated mesenchymal cells to osteoprogenitor cells, proliferation and differentiation of committed bone forming cells, extracellular matrix synthesis, mineralization of osteoid, maturation and remodeling of bone. These cellular events are precisely controlled and regulated by specific signaling molecules. Some of these like transforming growth factor beta (TGF-?), vascular endothelial growth factor (VEGF), bone morphogenetic proteins (BMP) and insulin like growth factors (IGF) are well conserved proteins involved in the initial response to injur

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Publication Date
Mon Aug 01 2022
Journal Name
Inorganic Chemistry Communications
Study to molecular insight into the role of aluminum nitride nanotubes on to deliver of 5-Fluorouracil (5FU) drug in smart drug delivery
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The adsorption process of 5-Fluorouracil (5FU) drugs on Aluminum nitride nanotubes surface (AlNNTs) have been evaluated through density functional theory (DFT). The DFT results show that the interaction of AlNNTs with the F atoms of 5FU drugs is strong due to the fact that the amount of adsorption energy was about − 29.65 kcal.mol−1. Conversely, the interaction of the 5FU through O atoms with the AlNNTs was weaker due to the lower value of adsorption energy. Also, based on the values of Gibbs free energy, the 5FU adsorption on the surfaces of AlNNTs was spontaneous. In addition, based on natural bond orbital (NBO) analysis, the direction of charge transfer was from fluorine’s σ orbitals of the drug to nitrogen’s and aluminum’s n*

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Publication Date
Sun Mar 13 2011
Journal Name
Baghdad Science Journal
Some A Survey Study On The Role of Women in Controlling Parasites Contaminated with Vegetables.
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Three hundred samples of washing water of vegetables were collected from women aged ( 15- 6o) years from different area in Baghdad governorate and its suburbs include two rural area ( Jaddria in Baghdad university and Al –Wagif in Rashdia) and two urbane area (Mansoure and Escan) . The samples were examined by precipitation method and then by staining method ( Lugols –Iodine stain) . The percentage of infection of intestinal parasites 36.3% include 15.3% for urban area and 57.3% in rural area and a significant difference was found between those groups . .The results showed also increased in the prevalence of parasitic infection in group age (15 -30) year .Also the results showed only 109 sample infected with eight specie

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Tax Exemptions and their impact in reducing the phenomenon of tax evasion: A field study
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The research aims to verifying the tax exemptions granted in accordance with the Iraqi tax legislations, showing their suitability for basic tax rules, and identifying their role to reduce the tax evasion phenomenon and the negative effects resulting therefrom, which arerepresented by a decrease in the proceeds of tax revenue and therefore leadings to a reduction of public revenues of the state. Also, the research tries to identify the ways to reduce cases of tax evasion due to their reflection positively on the public budgetof the state. The data of the research was collected through two models of questionnaires distributed to a sample of taxpayers from some professions and a sample of the tax administration staff. The research has reac

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Publication Date
Thu Nov 02 2023
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Appraising the Role of Pharmacists in Medication Reconciliation at Hospital Discharge: A Field-Based Study
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Objective: To measure the effect of the pharmacist-led medication reconciliation service before hospital discharge on preventing potential medication errors. Methods: This behavioral interventional study took place in a public teaching hospital in Iraq between December 2022 and January 2023. It included inpatients who were taking four or more medications upon discharge from the internal medicine ward and the cardiac care unit. The researcher provided the patients with a medication reconciliation form and reconciliation form (including medication regimen and pharmacist instructions) before discharging them home. Any discrepancies between the patients’ understanding and the actual medication recommendations prescribed by the physici

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